Method of designing addressable array suitable for detection of nucleic acid sequence differences using ligase detection reaction

ABSTRACT

The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The present invention further relates to an oligonucleotide array comprising of a support with the plurality of oligonucleotide probes immobilized on the support, a method of using the support to detect single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences, and a kit for such detection, which includes the support on which the oligonucleotides have been immobilized.

This application is a continuation of U.S. patent application Ser. No.15/096,446, filed Apr. 12, 2016, which is a continuation of U.S. patentapplication Ser. No. 13/947,777, filed Jul. 22, 2013, now U.S. Pat. No.9,340,834, issued on May 17, 2016, which is a division of U.S. patentapplication Ser. No. 12/252,169, filed Oct. 15, 2008, now U.S. Pat. No.8,492,085 issued on Jul. 23, 2013, which is a division of U.S. patentapplication Ser. No. 10/257,158, filed Apr. 1, 2004, now U.S. Pat. No.7,455,965 issued on Nov. 25, 2008, which is a national stage applicationunder 35 U.S.C. §371 PCT Application Serial No. PCT/US01/10958, filedApr. 4, 2001, which claims the benefit of U.S. Provisional PatentApplication Ser. No. 60/197,271, filed Apr. 14, 2000, each of which ishereby incorporated by reference in its entirety.

This invention was made with government support under grant numbersGM-41337-06, GM-43552-05, GM-42722-07, and GM-51628-02 awarded byNational Institutes of Health. The government has certain rights in thisinvention

FIELD OF THE INVENTION

The present invention is directed to a method of designing a pluralityof capture oligonucleotide probes for use on a support to whichcomplementary oligonucleotide probes will hybridize with littlemismatch, where the plural capture oligonucleotide probes have meltingtemperatures within a narrow range. Other aspects of the presentinvention relate to a support with the plurality of oligonucleotideprobes immobilized on the support, a method of using the support todetect single-base changes, insertions, deletions, or translocations ina plurality of target nucleotide sequences, and a kit for suchdetection, which includes the support on which the oligonucleotides havebeen immobilized.

BACKGROUND OF THE INVENTION Detection of Sequence Differences

Large-scale multiplex analysis of highly polymorphic loci is needed forpractical identification of individuals, e.g., for paternity testing andin forensic science (Reynolds et al., Anal. Chem., 63:2-15 (1991)), fororgan-transplant donor-recipient matching (Buyse et al., TissueAntigens, 41:1-14 (1993) and Gyllensten et al., PCR Meth. Appl, 1:91-98(1991)), for genetic disease diagnosis, prognosis, and pre-natalcounseling (Chamberlain et al., Nucleic Acids Res., 16:11141-11156(1988) and L. C. Tsui, Human Mutat., 1:197-203 (1992)), and the study ofoncogenic mutations (Hollstein et al., Science, 253:49-53 (1991)). Inaddition, the cost-effectiveness of infectious disease diagnosis bynucleic acid analysis varies directly with the multiplex scale in paneltesting. Many of these applications depend on the discrimination ofsingle-base differences at a multiplicity of sometimes closely spaceloci.

A variety of DNA hybridization techniques are available for detectingthe presence of one or more selected polynucleotide sequences in asample containing a large number of sequence regions. In a simplemethod, which relies on fragment capture and labeling, a fragmentcontaining a selected sequence is captured by hybridization to animmobilized probe. The captured fragment can be labeled by hybridizationto a second probe which contains a detectable reporter moiety.

Another widely used method is Southern blotting. In this method, amixture of DNA fragments in a sample are fractionated by gelelectrophoresis, then fixed on a nitrocellulose filter. By reacting thefilter with one or more labeled probes under hybridization conditions,the presence of bands containing the probe sequence can be identified.The method is especially useful for identifying fragments in arestriction-enzyme DNA digest which contain a given probe sequence, andfor analyzing restriction-fragment length polymorphisms (“RFLPs”).

Another approach to detecting the presence of a given sequence orsequences in a polynucleotide sample involves selective amplification ofthe sequence(s) by polymerase chain reaction. U.S. Pat. No. 4,683,202 toMullis, et al. and R. K. Saiki, et al., Science 230:1350 (1985). In thismethod, primers complementary to opposite end portions of the selectedsequence(s) are used to promote, in conjunction with thermal cycling,successive rounds of primer-initiated replication. The amplifiedsequence may be readily identified by a variety of techniques. Thisapproach is particularly useful for detecting the presence of low-copysequences in a polynucleotide-containing sample, e.g., for detectingpathogen sequences in a body-fluid sample.

More recently, methods of identifying known target sequences by probeligation methods have been reported. U.S. Pat. No. 4,883,750 to N. M.Whiteley, et al., D. Y. Wu, et al., Genomics 4:560 (1989), U. Landegren,et al., Science 241:1077 (1988), and E. Winn-Deen, et al., Clin. Chem.37:1522 (1991). In one approach, known as oligonucleotide ligation assay(“OLA”), two probes or probe elements which span a target region ofinterest are hybridized with the target region. Where the probe elementsmatch (basepair with) adjacent target bases at the confronting ends ofthe probe elements, the two elements can be joined by ligation, e.g., bytreatment with ligase. The ligated probe element is then assayed,evidencing the presence of the target sequence.

In a modification of this approach, the ligated probe elements act as atemplate for a pair of complementary probe elements. With continuedcycles of denaturation, hybridization, and ligation in the presence ofthe two complementary pairs of probe elements, the target sequence isamplified exponentially, i.e., exponentially allowing very small amountsof target sequence to be detected and/or amplified. This approach isreferred to as ligase chain reaction (“LCR”). F. Barany, “GeneticDisease Detection and DNA Amplification Using Cloned ThermostableLigase,” Proc. Nat'l Acad. Sci. USA, 88:189-93 (1991) and F. Barany,“The Ligase Chain Reaction (LCR) in a PCR World,” PCR Methods andApplications, 1:5-16 (1991).

Another scheme for multiplex detection of nucleic acid sequencedifferences is disclosed in U.S. Pat. No. 5,470,705 to Grossman et. al.where sequence-specific probes, having a detectable label and adistinctive ratio of charge/translational frictional drag, can behybridized to a target and ligated together. This technique was used inGrossman, et. al., “High-density Multiplex Detection of Nucleic AcidSequences: Oligonucleotide Ligation Assay and Sequence-codedSeparation,” Nucl. Acids Res. 22(21):4527-34 (1994) for the large scalemultiplex analysis of the cystic fibrosis transmembrane regulator gene.

Jou, et. al., “Deletion Detection in Dystrophin Gene by Multiplex GapLigase Chain Reaction and Immunochromatographic Strip Technology,” HumanMutation 5:86-93 (1995) relates to the use of a so called “gap ligasechain reaction” process to amplify simultaneously selected regions ofmultiple exons with the amplified products being read on animmunochromatographic strip having antibodies specific to the differenthaptens on the probes for each exon.

There is a growing need, e.g., in the field of genetic screening, formethods useful in detecting the presence or absence of each of a largenumber of sequences in a target polynucleotide. For example, as many as400 different mutations have been associated with cystic fibrosis. Inscreening for genetic predisposition to this disease, it is optimal totest all of the possible different gene sequence mutations in thesubject's genomic DNA, in order to make a positive identification of“cystic fibrosis”. It would be ideal to test for the presence or absenceof all of the possible mutation sites in a single assay. However, theprior-art methods described above are not readily adaptable for use indetecting multiple selected sequences in a convenient, automatedsingle-assay format.

Solid-phase hybridization assays require multiple liquid-handling steps,and some incubation and wash temperatures must be carefully controlledto keep the stringency needed for single-nucleotide mismatchdiscrimination. Multiplexing of this approach has proven difficult asoptimal hybridization conditions vary greatly among probe sequences.

Allele-specific PCR products generally have the same size, and a givenamplification tube is scored by the presence or absence of the productband in the gel lane associated with each reaction tube. Gibbs et al.,Nucleic Acids Res., 17:2437-2448 (1989). This approach requiressplitting the test sample among multiple reaction tubes with differentprimer combinations, multiplying assay cost. PCR has also discriminatedalleles by attaching different fluorescent dyes to competing allelicprimers in a single reaction tube (F. F. Chehab, et al., Proc. Natl.Acad. Sci. USA, 86:9178-9182 (1989)), but this route to multiplexanalysis is limited in scale by the relatively few dyes which can bespectrally resolved in an economical manner with existinginstrumentation and dye chemistry. The incorporation of bases modifiedwith bulky side chains can be used to differentiate allelic PCR productsby their electrophoretic mobility, but this method is limited by thesuccessful incorporation of these modified bases by polymerase, and bythe ability of electrophoresis to resolve relatively large PCR productswhich differ in size by only one of these groups. Livak et al., NucleicAcids Res., 20:4831-4837 (1989). Each PCR product is used to look foronly a single mutation, making multiplexing difficult.

Ligation of allele-specific probes generally has used solid-phasecapture (U. Landegren et al., Science, 241:1077-1080 (1988); Nickersonet al., Proc. Natl. Acad. Sci. USA, 87:8923-8927 (1990)) orsize-dependent separation (D. Y. Wu, et al., Genomics, 4:560-569 (1989)and F. Barany, Proc. Natl. Acad. Sci., 88:189-193 (1991)) to resolve theallelic signals, the latter method being limited in multiplex scale bythe narrow size range of ligation probes. The gap ligase chain reactionprocess requires an additional step—polymerase extension. The use ofprobes with distinctive ratios of charge/translational frictional dragtechnique to a more complex multiplex will either require longerelectrophoresis times or the use of an alternate form of detection.

The need thus remains for a rapid single assay format to detect thepresence or absence of multiple selected sequences in a polynucleotidesample.

Use of Oligonucleotide Arrays for Nucleic Acid Analysis

Ordered arrays of oligonucleotides immobilized on a solid support havebeen proposed for sequencing, sorting, isolating, and manipulating DNA.It has been recognized that hybridization of a cloned single-strandedDNA molecule to all possible oligonucleotide probes of a given lengthcan theoretically identify the corresponding complementary DNA segmentspresent in the molecule. In such an array, each oligonucleotide probe isimmobilized on a solid support at a different predetermined position.All the oligonucleotide segments in a DNA molecule can be surveyed withsuch an array.

One example of a procedure for sequencing DNA molecules using arrays ofoligonucleotides is disclosed in U.S. Pat. No. 5,202,231 to Drmanac, et.al. This involves application of target DNA to a solid support to whicha plurality of oligonucleotides are attached. Sequences are read byhybridization of segments of the target DNA to the oligonucleotides andassembly of overlapping segments of hybridized oligonucleotides. Thearray utilizes all possible oligonucleotides of a certain length between11 and 20 nucleotides, but there is little information about how thisarray is constructed. See also A. B. Chetverin, et. al., “Sequencing ofPools of Nucleic Acids on Oligonucleotide Arrays,” BioSystems 30: 215-31(1993); WO 92/16655 to Khrapko et. al.; Kuznetsova, et. al., “DNASequencing by Hybridization with Oligonucleotides Immobilized in Gel.Chemical Ligation as a Method of Expanding the Prospects for theMethod,” Mol. Biol. 28(20): 290-99(1994); M. A. Livits, et. al.,“Dissociation of Duplexes Formed by Hybridization of DNA withGel-Immobilized Oligonucleotides,” J. Biomolec. Struct. & Dynam. 11(4):783-812 (1994).

WO 89/10977 to Southern discloses the use of a support carrying an arrayof oligonucleotides capable of undergoing a hybridization reaction foruse in analyzing a nucleic acid sample for known point mutations,genomic fingerprinting, linkage analysis, and sequence determination.The matrix is formed by laying nucleotide bases in a selected pattern onthe support. This reference indicates that a hydroxyl linker group canbe applied to the support with the oligonucleotides being assembled by apen plotter or by masking.

WO 94/11530 to Cantor also relates to the use of an oligonucleotidearray to carry out a process of sequencing by hybridization. Theoligonucleotides are duplexes having overhanging ends to which targetnucleic acids bind and are then ligated to the non-overhanging portionof the duplex. The array is constructed by using streptavidin-coatedfilter paper which captures biotinylated oligonucleotides assembledbefore attachment.

WO 93/17126 to Chetverin uses sectioned, binary oligonucleotide arraysto sort and survey nucleic acids. These arrays have a constantnucleotide sequence attached to an adjacent variable nucleotidesequence, both bound to a solid support by a covalent linking moiety.The constant nucleotide sequence has a priming region to permitamplification by PCR of hybridized strands. Sorting is then carried outby hybridization to the variable region. Sequencing, isolating, sorting,and manipulating fragmented nucleic acids on these binary arrays arealso disclosed. In one embodiment with enhanced sensitivity, theimmobilized oligonucleotide has a shorter complementary regionhybridized to it, leaving part of the oligonucleotide uncovered. Thearray is then subjected to hybridization conditions so that acomplementary nucleic acid anneals to the immobilized oligonucleotide.DNA ligase is then used to join the shorter complementary region and thecomplementary nucleic acid on the array. There is little disclosure ofhow to prepare the arrays of oligonucleotides.

WO 92/10588 to Fodor et. al., discloses a process for sequencing,fingerprinting, and mapping nucleic acids by hybridization to an arrayof oligonucleotides. The array of oligonucleotides is prepared by a verylarge scale immobilized polymer synthesis which permits the synthesis oflarge, different oligonucleotides. In this procedure, the substratesurface is functionalized and provided with a linker group by whicholigonucleotides are assembled on the substrate. The regions whereoligonucleotides are attached have protective groups (on the substrateor individual nucleotide subunits) which are selectively activated.Generally, this involves imaging the array with light using a mask ofvarying configuration so that areas exposed are deprotected. Areas whichhave been deprotected undergo a chemical reaction with a protectednucleotide to extend the oligonucleotide sequence where imaged. A binarymasking strategy can be used to build two or more arrays at a giventime. Detection involves positional localization of the region wherehybridization has taken place. See also U.S. Pat. Nos. 5,324,633 and5,424,186 to Fodor et. al., U.S. Pat. Nos. 5,143,854 and 5,405,783 toPirrung, et. al., WO 90/15070 to Pirrung, et. al., A. C. Pease, et. al.,“Light-generated Oligonucleotide Arrays for Rapid DNA SequenceAnalysis”, Proc. Natl. Acad. Sci USA 91: 5022-26 (1994). K. L. Beattie,et. al., “Advances in Genosensor Research,” Clin. Chem. 41(5): 700-09(1995) discloses attachment of previously assembled oligonucleotideprobes to a solid support.

There are many drawbacks to the procedures for sequencing byhybridization to such arrays. Firstly, a very large number ofoligonucleotides must be synthesized. Secondly, there is poordiscrimination between correctly hybridized, properly matched duplexesand those which are mismatched. Finally, certain oligonucleotides willbe difficult to hybridize to under standard conditions, with sucholigonucleotides being capable of identification only through extensivehybridization studies.

The present invention is directed toward overcoming these deficienciesin the art.

SUMMARY OF THE INVENTION

The present invention is directed to a method of designing a pluralityof capture oligonucleotide probes for use on a support to whichcomplementary oligonucleotide probes will hybridize with littlemismatch, where the plural capture oligonucleotide probes have meltingtemperatures within a narrow range. The first step of the methodinvolves providing a first set of a plurality of tetramers of fournucleotides linked together, where (1) each tetramer within the setdiffers from all other tetramers in the set by at least two nucleotidebases, (2) no two tetramers within a set are complementary to oneanother, (3) no tetramers within a set are palindromic or dinucleotiderepeats, and (4) no tetramer within a set has one or less or three ormore G or C nucleotides. Groups of 2 to 4 of the tetramers from thefirst set are linked together to form a collection of multimer units.From the collection of multimer units, all multimer units formed fromthe same tetramer and all multimer units having a melting temperature in° C. of less than 4 times the number of tetramers forming a multimerunit are removed to form a modified collection of multimer units. Themodified collection of multimer units is arranged in a list in order ofmelting temperature. The order of the modified collection of multimerunits is randomized in 2° C. increments of melting temperature.Alternating multimer units in the list are then divided into first andsecond subcollections, each arranged in order of melting temperature.After the order of the second subcollection is inverted, the firstcollection is linked in order to the inverted second collection to forma collection of double multimer units. From the collection of doublemultimer units those units (1) having a melting temperature in ° C. lessthan 11 times the number of tetramers and more than 15 times the numberof tetramers, (2) double multimer units with the same 3 tetramers linkedtogether, and (3) double multimer units with the same 4 tetramers linkedtogether with or without interruption are removed, to form a modifiedcollection of double multimer units.

Another aspect of the present invention relates to an oligonucleotidearray which includes a support and a collection of double multimer unitoligonucleotides at different positions on the support so thatcomplementary oligonucleotides to be immobilized on the solid supportcan be captured at the different positions. The complementaryoligonucleotides will hybridize, within a narrow temperature range ofgreater than 24° C. with little mismatch, to members of the collectionof double multimer unit oligonucleotides, the double multimer unitoligonucleotides are formed from sets of tetramers where (1) eachtetramer within the set differs from all other tetramers in the set byat least two nucleotide bases, (2) no two tetramers within a set arecomplementary to one another, and (3) no tetramers within a set arepalindromic or dinucleotide repeats, and the collection of doublemultimer unit oligonucleotides has had the following oligonucleotidesremoved from it: (1) oligonucleotides having a melting temperature in °C. less than 12.5 times the number of tetramers and more than 14 timesthe number of tetramers, (2) double multimer units with the same 3tetramers linked together, and (3) multimer units with the same 4tetramers linked together with or without interruption.

Yet another aspect of the present invention relates to a method foridentifying one or more of a plurality of sequences differing by one ormore single-base changes, insertions, deletions, or translocations in aplurality of target nucleotide sequences. This method involves providinga sample potentially containing one or more target nucleotide sequenceswith a plurality of sequence differences. A plurality of oligonucleotideprobe sets are also provided with each set characterized by (a) a firstoligonucleotide probe, having a target-specific portion and anaddressable array-specific portion, and (b) a second oligonucleotideprobe, having a target-specific portion and a detectable reporter label.The oligonucleotide probes in a particular set are suitable for ligationtogether when hybridized adjacent to one another on a correspondingtarget nucleotide sequence, but have a mismatch which interferes withsuch ligation when hybridized to any other nucleotide sequence presentin the sample. A ligase is also provided with the sample, the pluralityof oligonucleotide probe sets, and the ligase being blended to form amixture. The mixture is subjected to one or more ligase detectionreaction cycles comprising a denaturation treatment, where anyhybridized oligonucleotides are separated from the target nucleotidesequences, and a hybridization treatment, where the oligonucleotideprobe sets hybridize at adjacent positions in a base-specific manner totheir respective target nucleotide sequences, if present in the sample,and ligate to one another to form a ligated product sequence containing(a) the addressable array-specific portion, (b) the target-specificportions connected together, and (c) the detectable reporter label. Theoligonucleotide probe sets may hybridize to nucleotide sequences in thesample other than their respective target nucleotide sequences but donot ligate together due to a presence of one or more mismatches andindividually separate during the denaturation treatment. A support isprovided with different capture oligonucleotides immobilized atdifferent positions, where the capture oligonucleotides have nucleotidesequences complementary to the addressable array-specific portions andare formed from a collection of double multimer unit oligonucleotides.The oligonucleotide with addressable array-specific portions willhybridize, within a narrow temperature range of more than 4 times thenumber of tetramers in the multimer unit with little mismatch, tomembers of the capture oligonuncleotides. The double multimer unitoligonucleotides are formed from sets of tetramers where (1) eachtetramer within the set differs from all other tetramers in the set byat least two nucleotide bases, (2) no two tetramers within a set arecomplementary to one another, and (3) no tetramers within a set arepalindromic or dinucleotide repeats. The collection of double multimerunit oligonucleotides has had the following oligonucleotides removedfrom it: (1) oligonucleotides having a melting temperature in ° C. ofless than 11 times the number of tetramers and more than 15 times thenumber of tetramers, (2) double multimer units with the same 3 tetramerslinked together, and (3) double multimer units with the same 4 tetramerslinked together with or without interruption, to form a modifiedcollection of double multimer units. After subjecting the mixture to oneor more ligase detection reaction cycles, the mixture is contacted withthe support under conditions effective to hybridize the addressablearray-specific portions to the capture oligonucleotides in abase-specific manner, thereby capturing the addressable array-specificportions on the support at the site with the complementary captureoligonucleotide. The reporter labels of ligated product sequencescaptured on the support at particular sites are detected, indicating thepresence of one or more target nucleotide sequences in the sample.

Another aspect of the present invention is directed to a kit foridentifying one or more of a plurality of sequences differing bysingle-base changes, insertions, deletions, or translocations in aplurality of target nucleotide sequences. In addition, to a ligase, thekit includes a plurality oligonucleotide probe sets, each characterizedby (a) a first oligonucleotide probe, having a target sequence-specificportion and an addressable array-specific portion, and (b) a secondoligonucleotide probe, having a target sequence-specific portion anddetectable reporter label, wherein the oligonucleotide probes in aparticular set are suitable for ligation together when hybridizedadjacent to one another on a respective target nucleotide sequence, buthave a mismatch which interferes with such ligation when hybridized toany other nucleotide sequence, present in the sample.

Also found in the kit is a support with different captureoligonucleotides immobilized at different positions, where the captureoligonucleotides have nucleotide sequences complementary to theaddressable array-specific portions and are formed from a collection ofdouble multimer unit oligonucleotides. The oligonucleotide withaddressable array-specific portions will hybridize, within a narrowtemperature range of greater than 4 times the number of tetramers in themultimer unit with little mismatch, to members of the captureoligonuncleotides. The double multimer unit oligonucleotides are formedfrom sets of tetramers where (1) each tetramer within the set differsfrom all other tetramers in the set by at least two nucleotide bases,(2) no two tetramers within a set are complementary to one another, and(3) no tetramers within a set are palindromic or dinucleotide repeats.The collection of double multimer unit oligonucleotides has had thefollowing oligonucleotides removed from it: (1) oligonucleotides havinga melting temperature in ° C. of less than 11 times the number oftetramers and more than 15 times then number of tetramers, (2) doublemultimer units with the same 3 tetramers linked together, and (3) doublemultimer units with the same 4 tetramers linked together with or withoutinterruption, where the capture oligonucleotides have nucleotidesequences complementary to the addressable array-specific portions.

Another aspect of the present invention relates to a method to avoidsynthesizing ligase detection reaction oligonucleotides that willinappropriately cross-hybridize to capture oligonucleotides on a solidsupport. This method includes comparing the ligase detection reactionoligonucleotides with the capture oligonucleotides and identifying anycapture oligonucleotides likely to cross-hybridize to the ligasedetection reaction oligonucleotides.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow diagram depicting polymerase chain reaction(“PCR”)/ligase detection reaction (“LDR”) processes, according to theprior art and the present invention, for detection of germlinemutations, such as point mutations.

FIG. 2 is a flow diagram depicting PCR/LDR processes, according to theprior art and the present invention, for detection of cancer-associatedmutations.

FIG. 3 is a schematic diagram depicting a PCR/LDR process, according tothe present invention, using addresses on the allele-specific probes fordetecting homo- or heterozygosity at two polymorphisms (i.e. alleledifferences) on the same gene.

FIG. 4 is a schematic diagram depicting a PCR/LDR process according tothe present invention, using addresses on common probes for detectinghomo- or heterozygosity at two polymorphisms (i.e. allele differences)on the same gene.

FIG. 5 is a schematic diagram depicting a PCR/LDR process, according tothe present invention, using addresses on the allele-specific probeswhich distinguishes all possible bases at a given site.

FIG. 6 is a schematic diagram depicting a PCR/LDR process, according tothe present invention, using addresses on the common probes whichdistinguishes all possible bases at a given site.

FIG. 7 is a schematic diagram depicting a PCR/LDR process, according tothe present invention, using addresses on the allele-specific probes fordetecting the presence of any possible base at two nearby sites.

FIG. 8 is a schematic diagram depicting a PCR/LDR process, according tothe present invention, using addresses on the common probes fordetecting the presence of any possible base at two nearby sites.

FIG. 9 is a schematic diagram of a PCR/LDR process, according to thepresent invention, using addresses on the allele-specific probes fordistinguishing insertions and deletions.

FIG. 10 is a schematic diagram of a PCR/LDR process, according to thepresent invention, using addresses on the common probes fordistinguishing insertions and deletions.

FIG. 11 is a schematic diagram of a PCR/LDR process, in accordance withthe present invention, using addresses on the allele-specific probes todetect a low abundance mutation (within a codon) in the presence of anexcess of normal sequence.

FIG. 12 is a schematic diagram of a PCR/LDR process, in accordance withthe present invention, using addresses on the common probes to detect alow abundance mutation (within a codon) in the presence of an excess ofnormal sequence.

FIG. 13 is a schematic diagram of a PCR/LDR process, in accordance withthe present invention, where the address is placed on the common probeand the allele differences are distinguished by different fluorescentsignals F1, F2, F3, and F4.

FIG. 14 is a schematic diagram of a PCR/LDR process, in accordance withthe present invention, where both adjacent and nearby alleles aredetected.

FIG. 15 is a schematic diagram of a PCR/LDR process, in accordance withthe present invention, where all possible single-base mutations for asingle codon are detected.

FIGS. 16A-P show the p53 chip hybridization and washing conditions.

FIGS. 17A-C show two alternative formats for oligonucleotide probecapture. In FIG. 17B, the addressable array-specific portions are on theallele-specific probe. Alleles are distinguished by capture offluorescent signals on addresses Z1 and Z2, respectively. In FIG. 17C,the addressable array-specific portions are on the common probe andalleles are distinguished by capture of fluorescent signals F1 and F2,which correspond to the two alleles, respectively.

FIG. 18 shows the chemical reactions for covalent modifications,grafting, oligomer attachments to solid supports.

FIG. 19 shows a design in accordance with the present invention using 36tetramers differing by at least 2 bases, which can be used to create aseries of unique 24-mers.

FIG. 20 shows an outline of the PCR/PCR/LDR method for detection ofmutations in BRCA1 and BRCA2.

FIGS. 21A-B show the multiplex LDR detection of 3 specific mutations inBRCA1 and BRCA2 in a gel-based assay.

FIG. 22 shows an outline of multiplex LDR detection of 3 specificmutations in BRCA1 and BRCA2 using an universal DNA microarray.

FIG. 23A-H show the LDR detection of 3 specific mutations in BRCA1 andBRCA2 on an addressable universal microarray.

FIG. 24A-H show p53 chip hybridization indicating the presence ofmutations in DNA from colon tumors.

FIGS. 25A-25MMMM show a list of 4633 capture oligonucleotides (SEQ IDNOS: 1-4633) produced in accordance with the present invention. One ofordinary skill in the art can readily envision the complementaryoligonucleotides corresponding to the capture oligonucleotides listed inFIGS. 25A-25MMMM.

FIGS. 26A-26J show a list of 465 capture oligonucleotides (SEQ ID NOS:1-465) produced in accordance with the present invention. One ofordinary skill in the art can readily envision the complementaryoligonucleotides corresponding to the capture oligonucleotides listed inFIGS. 26A-26J.

FIGS. 27A-27B show a list of 96 capture oligonucleotides (SEQ ID NOS:1-96) produced in accordance with the present invention. One of ordinaryskill in the art can readily envision the complementary oligonucleotidescorresponding to the capture oligonucleotides listed in FIGS. 27A-27B.

FIGS. 28A-28B show a list of 65 capture oligonucleotides (SEQ ID NOS:1-65) produced in accordance with the present invention. One of ordinaryskill in the art can readily envision the complementary oligonucleotidescorresponding to the capture oligonucleotides listed in FIGS. 28A-28B.

FIGS. 29A-29SSSS show a list of 4633 capture oligonucleotides (SEQ IDNOS: 4634-9266) (in the form of 20 mer PNAs) produced in accordance withthe present invention.

FIG. 30 shows a melting temperature (i.e. Tm) distribution for a list of96 capture oligonucleotides produced in accordance with the presentinvention.

FIG. 31 shows a melting temperature (i.e. Tm) distribution for a list of465 capture oligonucleotides produced in accordance with the presentinvention.

FIG. 32 shows a melting temperature (i.e. Tm) distribution for a list of4633 capture oligonucleotides produced in accordance with the presentinvention.

FIG. 33 shows a sorted melting temperature (i.e. Tm) distribution for alist of 4633 capture oligonucleotides produced in accordance with thepresent invention.

FIG. 34 shows the tetramer usage in the lists of 65, 96, 465, and 4633capture oligonucleotides produced in accordance with the presentinvention.

FIGS. 35A-T set forth a computer program for comparing a target sequencewith an array capture probe to insure that the latter will be designednot to hybridize to the former.

FIGS. 36A-H show the LDR detection of 7 specific mutations in K-ras onan addressable universal microarray.

DETAILED DESCRIPTION OF THE INVENTION AND DRAWINGS

The present invention is directed to a method of designing a pluralityof capture oligonucleotide probes for use on a support to whichcomplementary oligonucleotide probes will hybridize with littlemismatch, where the plural capture oligonucleotide probes have meltingtemperatures within a narrow range. The first step of the methodinvolves providing a first set of a plurality of tetramers of fournucleotides linked together, where (1) each tetramer within the setdiffers from all other tetramers in the set by at least two nucleotidebases, (2) no two tetramers within a set are complementary to oneanother, (3) no tetramers within a set are palindromic or dinucleotiderepeats, and (4) no tetramer within a set has one or less or three ormore G or C nucleotides. Groups of 2 to 4 of the tetramers from thefirst set are linked together to form a collection of multimer units.From the collection of multimer units, all multimer units formed fromthe same tetramer and all multimer units having a melting temperature in° C. of less than 4 times the number of tetramers forming a multimerunit are removed to form a modified collection of multimer units. Themodified collection of multimer units is arranged in a list in order ofmelting temperature. The order of the modified collection of multimerunits is randomized in 2° C. increments of melting temperature.Alternating multimer units in the list are then divided into first andsecond subcollections, each arranged in order of melting temperature.After the order of the second subcollection is inverted, the firstcollection is linked in order to the inverted second collection to forma collection of double multimer units. From the collection of doublemultimer units, those units (1) having a melting temperature in ° C.less than 11 times the number of tetramers and more than 15 times thenumber of tetramers, (2) double multimer units with the same 3 tetramerslinked together, and (3) double multimer units with the same 4 tetramerslinked together with or without interruption are removed, to form amodified collection of double multimer units.

Another aspect of the present invention relates to an oligonucleotidearray which includes a support and a collection of double multimer unitoligonucleotides at different positions on the support so thatcomplementary oligonucleotides to be immobilized on the solid supportcan be captured at the different positions. The complementaryoligonucleotides will hybridize, within a narrow temperature range ofgreater than 24° C. with little mismatch, to members of the collectionof double multimer unit oligonucleotides, the double multimer unitoligonucleotides are formed from sets of tetramers where (1) eachtetramer within the set differs from all other tetramers in the set byat least two nucleotide bases, (2) no two tetramers within a set arecomplementary to one another, and (3) no tetramers within a set arepalindromic or dinucleotide repeats, and the collection of doublemultimer unit oligonucleotides has had the following oligonucleotidesremoved from it: (1) oligonucleotides having a melting temperature in °C. less than 12.5 times the number of tetramers and more than 14 timesthe number of tetramers, (2) double multimer units with the same 3tetramers linked together, and (3) multimer units with the same 4tetramers linked together with or without interruption.

Yet another aspect of the present invention relates to a method foridentifying one or more of a plurality of sequences differing by one ormore single-base changes, insertions, deletions, or translocations in aplurality of target nucleotide sequences. This method involves providinga sample potentially containing one or more target nucleotide sequenceswith a plurality of sequence differences. A plurality of oligonucleotideprobe sets are also provided with each set characterized by (a) a firstoligonucleotide probe, having a target-specific portion and anaddressable array-specific portion, and (b) a second oligonucleotideprobe, having a target-specific portion and a detectable reporter label.The oligonucleotide probes in a particular set are suitable for ligationtogether when hybridized adjacent to one another on a correspondingtarget nucleotide sequence, but have a mismatch which interferes withsuch ligation when hybridized to any other nucleotide sequence presentin the sample. A ligase is also provided with the sample, the pluralityof oligonucleotide probe sets, and the ligase being blended to form amixture. The mixture is subjected to one or more ligase detectionreaction cycles comprising a denaturation treatment, where anyhybridized oligonucleotides are separated from the target nucleotidesequences, and a hybridization treatment, where the oligonucleotideprobe sets hybridize at adjacent positions in a base-specific manner totheir respective target nucleotide sequences, if present in the sample,and ligate to one another to form a ligated product sequence containing(a) the addressable array-specific portion, (b) the target-specificportions connected together, and (c) the detectable reporter label. Theoligonucleotide probe sets may hybridize to nucleotide sequences in thesample other than their respective target nucleotide sequences but donot ligate together due to a presence of one or more mismatches andindividually separate during the denaturation treatment. A support isprovided with capture oligonucleotides immobilized at differentpositions, where the capture oligonucleotides have nucleotide sequencescomplementary to the addressable array-specific portions and are formedfrom a collection of double multimer unit oligonucleotides. Theoligonucleotide with addressable array-specific portions will hybridize,within a narrow temperature range of more than 4 times the number oftetramers in the multimer unit with little mismatch, to members of thecapture oligonuncleotides. The double multimer unit oligonucleotides areformed from sets of tetramers where (1) each tetramer within the setdiffers from all other tetramers in the set by at least two nucleotidebases, (2) no two tetramers within a set are complementary to oneanother, and (3) no tetramers within a set are palindromic ordinucleotide repeats. The collection of double multimer unitoligonucleotides has had the following oligonucleotides removed from it:(1) oligonucleotides having a melting temperature in ° C. of less than11 times the number of tetramers and more than 15 times the number oftetramers, (2) double multimer units with the same 3 tetramers linkedtogether, and (3) double multimer units with the same 4 tetramers linkedtogether with or without interruption, to form a modified collection ofdouble multimer units. After subjecting the mixture to one or moreligase detection reaction cycles, the mixture is contacted with thesupport under conditions effective to hybridize the addressablearray-specific portions to the capture oligonucleotides in abase-specific manner, thereby capturing the addressable array-specificportions on the support at the site with the complementary captureoligonucleotide. The reporter labels of ligated product sequencescaptured on the support at particular sites are detected, indicating thepresence of one or more target nucleotide sequences in the sample.

Another aspect of the present invention is directed to a kit foridentifying one or more of a plurality of sequences differing bysingle-base changes, insertions, deletions, or translocations in aplurality of target nucleotide sequences. In addition, to a ligase, thekit includes a plurality oligonucleotide probe sets, each characterizedby (a) a first oligonucleotide probe, having a target sequence-specificportion and an addressable array-specific portion, and (b) a secondoligonucleotide probe, having a target sequence-specific portion anddetectable reporter label, wherein the oligonucleotide probes in aparticular set are suitable for ligation together when hybridizedadjacent to one another on a respective target nucleotide sequence, buthave a mismatch which interferes with such ligation when hybridized toany other nucleotide sequence, present in the sample. Also found in thekit is a support with different capture oligonucleotides immobilized atdifferent positions, where the capture oligonucleotides have nucleotidesequences complementary to the addressable array-specific portions andare formed from a collection of double multimer unit oligonucleotides.The oligonucleotide with addressable array-specific portions willhybridize, within a narrow temperature range of greater than 4 times thenumber of tetramers in the multimer unit with little mismatch, tomembers of the capture oligonuncleotides. The double multimer unitoligonucleotides are formed from sets of tetramers where (1) eachtetramer within the set differs from all other tetramers in the set byat least two nucleotide bases, (2) no two tetramers within a set arecomplementary to one another, and (3) no tetramers within a set arepalindromic or dinucleotide repeats. The collection of double multimerunit oligonucleotides has had the following oligonucleotides removedfrom it: (1) oligonucleotides having a melting temperature in ° C. ofless than 11 times the number of tetramers and more than 15 times thennumber of tetramers, (2) double multimer units with the same 3 tetramerslinked together, and (3) double multimer units with the same 4 tetramerslinked together with or without interruption, where the captureoligonucleotides have nucleotide sequences complementary to theaddressable array-specific portions.

Often, a number of different single-base mutations, insertions, ordeletions may occur at the same nucleotide position of the sequence ofinterest. The method provides for having an oligonucleotide set, wherethe second oligonucleotide probe is common and contains the detectablelabel, and the first oligonucleotide probe has different addressablearray-specific portions and target-specific portions. The firstoligonucleotide probe is suitable for ligation to a second adjacentoligonucleotide probe at a first ligation junction, when hybridizedwithout mismatch, to the sequence in question. Different first adjacentoligonucleotide probes would contain different discriminating base(s) atthe junction where only a hybridization without mismatch at the junctionwould allow for ligation. Each first adjacent oligonucleotide wouldcontain a different addressable array-specific portion, and, thus,specific base changes would be distinguished by capture at differentaddresses. In this scheme, a plurality of different captureoligonucleotides are attached at different locations on the solidsupport for multiplex detection of additional nucleic acid sequencesdiffering from other nucleic acids by at least a single base.Alternatively, the first oligonucleotide probe contains commonaddressable array-specific portions, and the second oligonucleotideprobes have different detectable labels and target-specific portions.

Such arrangements permit multiplex detection of additional nucleic acidsequences differing from other nucleic acids by at least a single base.The nucleic acids sequences can be on the same or different alleles whencarrying out such multiplex detection.

The present invention also relates to a kit for carrying out the methodof the present invention which includes the ligase, the plurality ofdifferent oligonucleotide probe sets, and the solid support withimmobilized capture oligonucleotides. Primers for preliminaryamplification of the target nucleotide sequences may also be included inthe kit. If amplification is by polymerase chain reaction, polymerasemay also be included in the kit.

FIGS. 1 and 2 show flow diagrams of the process of the present inventioncompared to a prior art ligase detection reaction utilizing capillary orgel electrophoresis/fluorescent quantification. FIG. 1 relates todetection of a germline mutation detection, while FIG. 2 shows thedetection of cancer.

FIG. 1 depicts the detection of a germline point mutation, such as thep53 mutations responsible for Li-Fraumeni syndrome. In step 1, after DNAsample preparation, exons 5-8 are PCR amplified using Taq (i.e. Thermusaquaticus) polymerase under hot start conditions. At the end of thereaction, Taq polymerase is degraded by treatment with Proteinase K.Products are diluted 20-fold in step 2 into fresh LDR buffer containingallele-specific and common LDR probes. A tube generally contains about500 fmoles of each primer. In step 3, the ligase detection reaction isinitiated by addition of Taq ligase under hot start conditions. The LDRprobes ligate to their adjacent probes only in the presence of targetsequence which gives perfect complementarity at the junction site. Theproducts may be detected in two different formats. In the first format4a., used in the prior art, fluorescently-labeled LDR probes containdifferent length poly A or hexaethylene oxide tails. Thus, each LDRproduct, resulting from ligation to normal DNA with a slightly differentmobility, yields a ladder of peaks. A germline mutation would generate anew peak on the electrophorogram. The size of the new peak willapproximate the amount of the mutation present in the original sample;0% for homozygous normal, 50% for heterozygous carrier, or 100% forhomozygous mutant. In the second format 4b., in accordance with thepresent invention, each allele-specific probe contains e.g., 24additional nucleotide bases on their 5′ ends. These sequences are uniqueaddressable sequences which will specifically hybridize to theircomplementary address sequences on an addressable array. In the LDRreaction, each allele-specific probe can ligate to its adjacentfluorescently labeled common probe in the presence of the correspondingtarget sequence. Wild type and mutant alleles are captured on adjacentaddresses on the array. Unreacted probes are washed away. The black dotsindicate 100% signal for the wild type allele. The white dots indicate0% signal for the mutant alleles. The shaded dots indicate the oneposition of germline mutation, 50% signal for each allele.

FIG. 2 depicts detection of somatic cell mutations in the p53 tumorsuppressor gene but is general for all low sensitivity mutationdetection. In step 1, DNA samples are prepared and exons 5-9 are PCRamplified as three fragments using fluorescent PCR primers. This allowsfor fluorescent quantification of PCR products in step 2 using capillaryor gel electrophoresis. In step 3, the products are spiked with a 1/100dilution of marker DNA (for each of the three fragments). This DNA ishomologous to wild type DNA, except it contains a mutation which is notobserved in cancer cells, but which may be readily detected with theappropriate LDR probes. The mixed DNA products in step 4 are diluted20-fold into buffer containing all the LDR probes which are specificonly to mutant or marker alleles. In step 5, the ligase detectionreaction is initiated by addition of Taq ligase under hot startconditions. The LDR probes ligate to their adjacent probes only in thepresence of target sequences which give perfect complementarity at thejunction site. The products may be detected in the same two formatsdescribed in FIG. 1. In the format of step 6a, which is used in theprior art, products are separated by capillary or gel electrophoresis,and fluorescent signals are quantified. Ratios of mutant peaks to markerpeaks give approximate amount of cancer mutations present in theoriginal sample divided by 100. In the format of step 6b, in accordancewith the present invention, products are detected by specifichybridization to complementary sequences on an addressable array. Ratiosof fluorescent signals in mutant dots to marker dots give theapproximate amount of cancer mutations present in the original sampledivided by 100.

The ligase detection reaction process, in accordance with the presentinvention, is best understood by referring to FIGS. 3-15. It isdescribed generally in WO 90/17239 to Barany et al., F. Barany et al.,“Cloning, Overexpression and Nucleotide Sequence of a Thermostable DNALigase-encoding Gene,” Gene, 109:1-11 (1991), and F. Barany, “GeneticDisease Detection and DNA Amplification Using Cloned ThermostableLigase,” Proc. Natl. Acad. Sci. USA, 88:189-193 (1991), the disclosuresof which are hereby incorporated by reference. In accordance with thepresent invention, the ligase detection reaction can use 2 sets ofcomplementary oligonucleotides. This is known as the ligase chainreaction which is described in the 3 immediately preceding references,which are hereby incorporated by reference. Alternatively, the ligasedetection reaction can involve a single cycle which is known as theoligonucleotide ligation assay. See Landegren, et al., “ALigase-Mediated Gene Detection Technique,” Science 241:1077-80 (1988);Landegren, et al., “DNA Diagnostics—Molecular Techniques andAutomation,” Science 242:229-37 (1988); and U.S. Pat. No. 4,988,617 toLandegren, et al.

During the ligase detection reaction phase of the process, thedenaturation treatment is carried out at a temperature of 80-105° C.,while hybridization takes place at 50-85° C. Each cycle comprises adenaturation treatment and a thermal hybridization treatment which intotal is from about one to five minutes long. Typically, the ligationdetection reaction involves repeatedly denaturing and hybridizing for 2to 50 cycles. The total time for the ligase detection reaction phase ofthe process is 1 to 250 minutes.

The oligonucleotide probe sets can be in the form of ribonucleotides,deoxynucleotides, modified ribonucleotides, modifieddeoxyribonucleotides, peptide nucleotide analogues, modified peptidenucleotide analogues, modified phosphate-sugar-backboneoligonucleotides, nucleotide analogs, and mixtures thereof.

In one variation, the oligonucleotides of the oligonucleotide probe setseach have a hybridization or melting temperature (i.e. T_(m)) of 66-70°C. These oligonucleotides are 20-28 nucleotides long.

It may be desirable to destroy chemically or enzymatically unconvertedLDR oligonucleotide probes that contain addressable nucleotidearray-specific portions prior to capture of the ligation products on aDNA array. Such unconverted probes will otherwise compete with ligationproducts for binding at the addresses on the array of the solid supportwhich contain complementary sequences. Destruction can be accomplishedby utilizing an exonuclease, such as exonuclease III (L-H Guo and R. Wu,Methods in Enzymology 100:60-96 (1985), which is hereby incorporated byreference) in combination with LDR probes that are blocked at the endsand not involved with ligation of probes to one another. The blockingmoiety could be a reporter group or a phosphorothioate group. T. T.Nikiforow, et al., “The Use of Phosphorothioate Primers and ExonucleaseHydrolysis for the Preparation of Single-stranded PCR Products and theirDetection by Solid-phase Hybridization,” PCR Methods and Applications,3:p. 285-291 (1994), which is hereby incorporated by reference. Afterthe LDR process, unligated probes are selectively destroyed byincubation of the reaction mixture with the exonuclease. The ligatedprobes are protected due to the elimination of free 3′ ends which arerequired for initiation of the exonuclease reaction. This approachresults in an increase in the signal-to-noise ratio, especially wherethe LDR reaction forms only a small amount of product. Since unligatedoligonucleotides compete for capture by the capture oligonucleotide,such competition with the ligated oligonucleotides lowers the signal. Anadditional advantage of this approach is that unhybridizedlabel-containing sequences are degraded and, therefore, are less able tocause a target-independent background signal, because they can beremoved more easily from the DNA array by washing.

The oligonucleotide probe sets, as noted above, have a reporter labelsuitable for detection. Useful labels include chromophores, fluorescentmoieties, enzymes, antigens, heavy metals, magnetic probes, dyes,phosphorescent groups, radioactive materials, chemiluminescent moieties,and electrochemical detecting moieties. The capture oligonucleotides canbe in the form of ribonucleotides, deoxyribonucleotides, modifiedribonucleotides, modified deoxyribonucleotides, peptide nucleotideanalogues, modified peptide nucleotide analogues, modifiedphosphate-sugar backbone oligonucleotides, nucleotide analogues, andmixtures thereof. Where the process of the present invention involvesuse of a plurality of oligonucleotide sets, the second oligonucleotideprobes can be the same, while the addressable array-specific portions ofthe first oligonucleotide probes differ. Alternatively, the addressablearray-specific portions of the first oligonucleotide probes may be thesame, while the reporter labels of the second oligonucleotide probes aredifferent.

Prior to the ligation detection reaction phase of the present invention,the sample is preferably amplified by an initial target nucleic acidamplification procedure. This increases the quantity of the targetnucleotide sequence in the sample. For example, the initial targetnucleic acid amplification may be accomplished using the polymerasechain reaction process, self-sustained sequence replication, or Q-βreplicase-mediated RNA amplification. The polymerase chain reactionprocess is the preferred amplification procedure and is fully describedin H. Erlich, et. al., “Recent Advances in the Polymerase ChainReaction,” Science 252: 1643-50 (1991); M. Innis, et. al., PCRProtocols: A Guide to Methods and Applications, Academic Press: New York(1990); and R. Saiki, et. al., “Primer-directed Enzymatic Amplificationof DNA with a Thermostable DNA Polymerase,” Science 239: 487-91 (1988),which are hereby incorporated by reference. J. Guatelli, et. al.,“Isothermal, in vitro Amplification of Nucleic Acids by a MultienzymeReaction Modeled After Retroviral Replication,” Proc. Natl. Acad. Sci.USA 87: 1874-78 (1990), which is hereby incorporated by reference,describes the self-sustained sequence replication process. The Q-βreplicase-mediated RNA amplification is disclosed in F. Kramer, et. al.,“Replicatable RNA Reporters,” Nature 339: 401-02 (1989), which is herebyincorporated by reference.

The use of the polymerase chain reaction process and then the ligasedetection process, in accordance with the present invention, is shown inFIG. 3. Here, homo- or heterozygosity at two polymorphisms (i.e. alleledifferences) are on the same gene. Such allele differences canalternatively be on different genes.

As shown in FIG. 3, the target nucleic acid, when present in the form ofa double stranded DNA molecule is denatured to separate the strands.This is achieved by heating to a temperature of 80-105° C. Polymerasechain reaction primers are then added and allowed to hybridize to thestrands, typically at a temperature of 20-85° C. A thermostablepolymerase (e.g., Thermus aquaticus polymerase) is also added, and thetemperature is then adjusted to 50-85° C. to extend the primer along thelength of the nucleic acid to which the primer is hybridized. After theextension phase of the polymerase chain reaction, the resulting doublestranded molecule is heated to a temperature of 80-105° C. to denaturethe molecule and to separate the strands. These hybridization,extension, and denaturation steps may be repeated a number of times toamplify the target to an appropriate level.

Once the polymerase chain reaction phase of the process is completed,the ligation detection reaction phase begins, as shown in FIG. 3. Afterdenaturation of the target nucleic acid, if present as a double strandedDNA molecule, at a temperature of 80-105° C., preferably 94° C.,ligation detection reaction oligonucleotide probes for one strand of thetarget nucleotide sequence are added along with a ligase (for example,as shown in FIG. 3, a thermostable ligase like Thermus aquaticusligase). The oligonucleotide probes are then allowed to hybridize to thetarget nucleic acid molecule and ligate together, typically, at atemperature of 45-85° C., preferably, 65° C. When there is perfectcomplementarity at the ligation junction, the oligonucleotides can beligated together. Where the variable nucleotide is T or A, the presenceof T in the target nucleotide sequence will cause the oligonucleotideprobe with the addressable array-specific portion Z1 to ligate to theoligonucleotide probe with the reporter label F, and the presence of Ain the target nucleotide sequence will cause the oligonucleotide probewith the addressable array-specific portion Z2 to ligate to theoligonucleotide probe with reporter label F. Similarly, where thevariable nucleotide is A or G, the presence of T in the targetnucleotide sequence will cause the oligonucleotide probe withaddressable array-specific portion Z4 to ligate to the oligonucleotideprobe with the reporter label F, and the presence of C in the targetnucleotide sequence will cause the oligonucleotide probe with theaddressable array-specific portion Z3 to ligate to the oligonucleotideprobe with reporter label F. Following ligation, the material is againsubjected to denaturation to separate the hybridized strands. Thehybridization/ligation and denaturation steps can be carried through oneor more cycles (e.g., 1 to 50 cycles) to amplify the target signal.Fluorescent ligation products (as well as unligated oligonucleotideprobes having an addressable array-specific portion) are captured byhybridization to capture probes complementary to portions Z1, Z2, Z3,and Z4 at particular addresses on the addressable arrays. The presenceof ligated oligonucleotides is then detected by virtue of the label Foriginally on one of the oligonucleotides. In FIG. 3, ligated productsequences hybridize to the array at addresses with captureoligonucleotides complementary to addressable array-specific portions Z1and Z3, while unligated oligonucleotide probes with addressablearray-specific portions Z2 and Z4 hybridize to their complementarycapture oligonucleotides. However, since only the ligated productsequences have label F, only their presence is detected.

FIG. 4 is similar to FIG. 3 except that in FIG. 4, the commonoligonucleotide probe has an address-specific portion, while theallele-specific probes have different labels.

FIG. 5 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, which distinguishes any possible base at a givensite. Appearance of fluorescent signal at the addresses complementary toaddressable array-specific portions Z1, Z2, Z3, and Z4 indicates thepresence of A, G, C, and T alleles in the target nucleotide sequence,respectively. Here, the presence of the A and C alleles in the targetnucleotide sequences is indicated due to the fluorescence at theaddresses on the solid support with capture oligonucleotide probescomplementary to portions Z1 and Z3, respectively. Note that in FIG. 5the addressable array-specific portions are on the discriminatingoligonucleotide probes, and the discriminating base is on the 3′ end ofthese probes.

FIG. 6 is similar to FIG. 5, except that in FIG. 6, the commonoligonucleotide probe has the address-specific portion, while theallele-specific probes have different labels.

FIG. 7 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, for detecting the presence of any possible base attwo nearby sites. Here, the LDR probes are able to overlap, yet arestill capable of ligating provided there is perfect complementarity atthe junction. This distinguishes LDR from other approaches, such asallele-specific PCR where overlapping primers would interfere with oneanother. In FIG. 7, the first nucleotide position is heterozygous at theA and C alleles, while the second nucleotide position is heterozygous tothe G, C, and T alleles. As in FIG. 5, the addressable array-specificportions are on the discriminating oligonucleotide probes, and thediscriminating base is on the 3′ end of these probes. The reporter group(e.g., the fluorescent label) is on the 3′ end of the commonoligonucleotide probes. This is possible for example with the 21hydroxylase gene, where each individual has 2 normal and 2 pseudogenes,and, at the intron 2 splice site (nucleotide 656), there are 3 possiblesingle bases (G, A, and C). Also, this can be used to detect lowabundance mutations in HIV infections which might indicate emergence ofdrug resistant (e.g., to AZT) strains. Returning to FIG. 7, appearanceof fluorescent signal at the addresses complementary to addressablearray-specific portions Z1, Z2, Z3, Z4, Z5, Z6, Z7, and Z8 indicates thepresence of the A, G, C, and T, respectively, in the site heterozygousat the A and C alleles, and A, G, C, and T, respectively, in the siteheterozygous at the G, C, and T alleles.

FIG. 8 is similar to FIG. 7, except that in FIG. 8, the commonoligonucleotide probes have the address-specific portions, while theallele specific probes have different labels.

FIG. 9 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, where insertions (top left set of probes) anddeletions (bottom right set of probes) are distinguished. On the left,the normal sequence contains 5 A's in a polyA tract. The mutant sequencehas an additional 2As inserted into the tract. Therefore, the LDRproducts with addressable array-specific portions Z1 (representing thenormal sequence) and Z3 (representing a 2 base pair insertion) would befluorescently labeled by ligation to the common probe. While the LDRprocess (e.g., using a thermostable ligase enzyme) has no difficultydistinguishing single base insertions or deletions in mononucleotiderepeats, allele-specific PCR is unable to distinguish such differences,because the 3′ base remains the same for both alleles. On the right, thenormal sequence is a (CA)5 repeat (i.e. CACACACACA (SEQ ID NO: 9267)).The mutant contains two less CA bases than the normal sequence (i.e.CACACA). These would be detected as fluorescent LDR products at theaddressable array-specific portions Z8 (representing the normalsequence) and Z6 (representing the 2 CA deletion) addresses. Theresistance of various infectious agents to drugs can also be determinedusing the present invention. In FIG. 9, the presence of ligated productsequences, as indicated by fluorescent label F, at the address havingcapture oligonucleotides complementary to Z1 and Z3 demonstrates thepresence of both the normal and mutant poly A sequences. Similarly, thepresence of ligated product sequences, as indicated by fluorescent labelF, at the address having capture oligonucleotides complementary to Z6and Z8 demonstrates the presence of both the normal CA repeat and asequence with one repeat unit deleted.

FIG. 10 is similar to FIG. 9, except that in FIG. 10, the commonoligonucleotide probes have the address-specific portions, while theallele-specific probes have different labels.

FIG. 11 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, using addressable array-specific portions to detect alow abundance mutation in the presence of an excess of normal sequence.FIG. 11 shows codon 12 of the K-ras gene, sequence GGT, which codes forglycine (“Gly”). A small percentage of the cells contain the G to Amutation in GAT, which codes for aspartic acid (“Asp”). The LDR probesfor wild-type (i.e. normal sequences) are missing from the reaction. Ifthe normal LDR probes (with the discriminating base=G) were included,they would ligate to the common probes and overwhelm any signal comingfrom the mutant target. Instead, as shown in FIG. 11, the existence of aligated product sequence with fluorescent label F at the address with acapture oligonucleotide complementary to addressable array-specificportion Z4 indicates the presence of the aspartic acid encoding mutant.

FIG. 12 is similar to FIG. 11, except that in FIG. 12, the commonoligonucleotide probes have address-specific portions, while theallele-specific probes have different labels.

FIG. 13 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, where the addressable array-specific portion isplaced on the common oligonucleotide probe, while the discriminatingoligonucleotide probe has the reporter label. Allele differences aredistinguished by different fluorescent signals, F1, F2, F3, and F4. Thismode allows for a more dense use of the arrays, because each position ispredicted to light up with some group. It has the disadvantage ofrequiring fluorescent groups which have minimal overlap in theiremission spectra and will require multiple scans. It is not ideallysuitable for detection of low abundance alleles (e.g., cancer associatedmutations).

FIG. 14 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, where both adjacent and nearby alleles are detected.The adjacent mutations are right next to each other, and one set ofoligonucleotide probes discriminates the bases on the 3′ end of thejunction (by use of different addressable array-specific portions Z1,Z2, Z3, and Z4), while the other set of oligonucleotide probesdiscriminates the bases on the 5′ end of the junction (by use ofdifferent fluorescent reporter labels F1, F2, F3, and F4). In FIG. 14,codons in a disease gene (e.g. CFTR for cystic fibrosis) encoding Glyand arginine (“Arg”), respectively, are candidates for germlinemutations. The detection results in FIG. 14 show the Gly (GGA; indicatedby the ligated product sequence having portion Z2 and label F2) has beenmutated to glutamic acid (“Glu”) (GAA; indicated by the ligated productsequence having portion Z2 and label F1), and the Arg (CGG; indicated bythe ligated product sequence having portion Z7 and label F2) has beenmutated to tryptophan (“Trp”) (TGG; indicated by the ligated productsequence with portion Z8 and label F2). Therefore, the patient is acompound heterozygous individual (i.e. with allele mutations in bothgenes) and will have the disease.

FIG. 15 is a flow diagram of a PCR/LDR process, in accordance with thepresent invention, where all possible single-base mutations for a singlecodon are detected. Most amino acid codons have a degeneracy in thethird base, thus the first two positions can determine all the possiblemutations at the protein level. These amino acids include arginine,leucine, serine, threonine, proline, alanine, glycine, and valine.However, some amino acids are determined by all three bases in the codonand, thus, require the oligonucleotide probes to distinguish mutationsin 3 adjacent positions. By designing four oligonucleotide probescontaining the four possible bases in the penultimate position to the 3′end, as well as designing an additional four capture oligonucleotidescontaining the four possible bases at the 3′ end, as shown in FIG. 15,this problem has been solved. The common oligonucleotide probes with thereporter labels only have two fluorescent groups which correspond to thecodon degeneracies and distinguish between different ligated productsequences which are captured at the same array address. For example, asshown in FIG. 15, the presence of a glutamine (“Gln”) encoding codon(i.e., CAA and CAG) is indicated by the presence of a ligated productsequence containing portion Z1 and label F2. Likewise, the existence ofa Gln to histidine (“His”) encoding mutation (coded by the codon CAC) isindicated by the presence of ligated product sequences with portion Z1and label F2 and with portion Z7 and label F2 There is an internalredundancy built into this assay due to the fact that primers Z1 and Z7have the identical sequence.

A particularly important aspect of the present invention is itscapability to quantify the amount of target nucleotide sequence in asample. This can be achieved in a number of ways by establishingstandards which can be internal (i.e. where the standard establishingmaterial is amplified and detected with the sample) or external (i.e.where the standard establishing material is not amplified, and isdetected with the sample).

In accordance with one quantification method, the signal generated bythe reporter label, resulting from capture of ligated product sequencesproduced from the sample being analyzed, are detected. The strength ofthis signal is compared to a calibration curve produced from signalsgenerated by capture of ligated product sequences in samples with knownamounts of target nucleotide sequence. As a result, the amount of targetnucleotide sequence in the sample being analyzed can be determined. Thistechnique involves use of an external standard.

Another quantification method, in accordance with the present invention,relates to an internal standard. Here, a known amount of one or moremarker target nucleotide sequences are added to the sample. In addition,a plurality of marker-specific oligonucleotide probe sets are addedalong with the ligase, the previously-discussed oligonucleotide probesets, and the sample to a mixture. The marker-specific oligonucleotideprobe sets have (1) a first oligonucleotide probe with a target-specificportion complementary to the marker target nucleotide sequence and anaddressable array-specific portion complementary to captureoligonucleotides on the support and (2) a second oligonucleotide probewith a target-specific portion complementary to the marker targetnucleotide sequence and a detectable reporter label. The oligonucleotideprobes in a particular marker-specific oligonucleotide set are suitablefor ligation together when hybridized adjacent to one another on acorresponding marker target nucleotide sequence. However, there is amismatch which interferes with such ligation when hybridized to anyother nucleotide sequence present in the sample or added markersequences. The presence of ligated product sequences captured on thesupport is identified by detection of reporter labels. The amount oftarget nucleotide sequences in the sample is then determined bycomparing the amount of captured ligated product generated from knownamounts of marker target nucleotide sequences with the amount of otherligated product sequences captured.

Another quantification method in accordance with the present inventioninvolves analysis of a sample containing two or more of a plurality oftarget nucleotide sequences with a plurality of sequence differences.Here, ligated product sequences corresponding to the target nucleotidesequences are detected and distinguished by any of thepreviously-discussed techniques. The relative amounts of the targetnucleotide sequences in the sample are then quantified by comparing therelative amounts of captured ligated product sequences generated. Thisprovides a quantitative measure of the relative level of the targetnucleotide sequences in the sample.

The ligase detection reaction process phase of the present invention canbe preceded by the ligase chain reaction process to achieveoligonucleotide product amplification. This process is fully describedin F. Barany, et. al., “Cloning, Overexpression and Nucleotide Sequenceof a Thermostable DNA Ligase-encoding Gene,” Gene 109: 1-11 (1991) andF. Barany, “Genetic Disease Detection and DNA Amplification Using ClonedThermostable Ligase,” Proc. Natl. Acad. Sci. USA 88: 189-93 (1991),which are hereby incorporated by reference. Instead of using the ligasechain reaction to achieve amplification, a transcription-basedamplifying procedure can be used.

The preferred thermostable ligase is that derived from Thermusaquaticus. This enzyme can be isolated from that organism. M. Takahashi,et al., “Thermophillic DNA Ligase,” J. Biol. Chem. 259:10041-47 (1984),which is hereby incorporated by reference. Alternatively, it can beprepared recombinantly. Procedures for such isolation as well as therecombinant production of Thermus aquaticus ligase (and Thermusthemophilus ligase) are disclosed in WO 90/17239 to Barany, et. al., andF. Barany, et al., “Cloning, Overexpression and Nucleotide Sequence of aThermostable DNA-Ligase Encoding Gene,” Gene 109:1-11 (1991), which arehereby incorporated by reference. These references contain completesequence information for this ligase as well as the encoding DNA. Othersuitable ligases include E. coli ligase, T4 ligase, Thermus sp. AK16ligase, Aquifex aeolicus ligase, Thermotoga maritima ligase, andPyrococcus ligase.

The ligation amplification mixture may include a carrier DNA, such assalmon sperm DNA.

The hybridization step, which is preferably a thermal hybridizationtreatment, discriminates between nucleotide sequences based on adistinguishing nucleotide at the ligation junctions. The differencebetween the target nucleotide sequences can be, for example, a singlenucleic acid base difference, a nucleic acid deletion, a nucleic acidinsertion, or rearrangement. Such sequence differences involving morethan one base can also be detected. Preferably, the oligonucleotideprobe sets have substantially the same length so that they hybridize totarget nucleotide sequences at substantially similar hybridizationconditions. As a result, the process of the present invention is able todetect infectious diseases, genetic diseases, and cancer. It is alsouseful in environmental monitoring, forensics, and food science.

A wide variety of infectious diseases can be detected by the process ofthe present invention. Typically, these are caused by bacterial, viral,parasite, and fungal infectious agents. The resistance of variousinfectious agents to drugs can also be determined using the presentinvention.

Bacterial infectious agents which can be detected by the presentinvention include Escherichia coli, Salmonella, Shigella, Klebsiella,Pseudomonas, Listeria monocytogenes, Mycobacterium tuberculosis,Mycobacterium avium-intracellulare, Yersinia, Francisella, Pasteurella,Brucella, Clostridia, Bordetella pertussis, Bacteroides, Staphylococcusaureus, Streptococcus pneumonia, B-Hemolytic strep., Corynebacteria,Legionella, Mycoplasma, Ureaplasma, Chlamydia, Neisseria gonorrhea,Neisseria meningitides, Hemophilus influenza, Enterococcus faecalis,Proteus vulgaris, Proteus mirabilis, Helicobacter pylori, Treponemapalladium, Borrelia burgdorferi, Borrelia recurrentis, Rickettsialpathogens, Nocardia, and Acitnomycetes.

Fungal infectious agents which can be detected by the present inventioninclude Cryptococcus neoformans, Blastomyces dermatitidis, Histoplasmacapsulatum, Coccidioides immitis, Paracoccicioides brasiliensis, Candidaalbicans, Aspergillus fumigautus, Phycomycetes (Rhizopus), Sporothrixschenckii, Chromomycosis, and Maduromycosis.

Viral infectious agents which can be detected by the present inventioninclude human immunodeficiency virus, human T-cell lymphocytotrophicvirus, hepatitis viruses (e.g., Hepatitis B Virus and Hepatitis CVirus), Epstein-Barr Virus, cytomegalovirus, human papillomaviruses,orthomyxo viruses, paramyxo viruses, adenoviruses, corona viruses,rhabdo viruses, polio viruses, toga viruses, bunya viruses, arenaviruses, rubella viruses, and reo viruses.

Parasitic agents which can be detected by the present invention includePlasmodium falciparum, Plasmodium malaria, Plasmodium vivax, Plasmodiumovale, Onchoverva volvulus, Leishmania, Trypanosoma spp., Schistosomaspp., Entamoeba histolytica, Cryptosporidium, Giardia spp., Trichimonasspp., Balatidium coli, Wuchereria bancrofti, Toxoplasma spp., Enterobiusvermicularis, Ascaris lumbricoides, Trichuris trichiura, Dracunculusmedinesis, trematodes, Diphyllobothrium latum, Taenia spp., Pneumocystiscarinii, and Necator americanis.

The present invention is also useful for detection of drug resistance byinfectious agents. For example, vancomycin-resistant Enterococcusfaecium, methicillin-resistant Staphylococcus aureus,penicillin-resistant Streptococcus pneumoniae, multi-drug resistantMycobacterium tuberculosis, and AZT-resistant human immunodeficiencyvirus can all be identified with the present invention.

Genetic diseases can also be detected by the process of the presentinvention. This can be carried out by prenatal screening for chromosomaland genetic aberrations or post natal screening for genetic diseases.Examples of detectable genetic diseases include: 21 hydroxylasedeficiency, cystic fibrosis, Fragile X Syndrome, Turner Syndrome,Duchenne Muscular Dystrophy, Down Syndrome or other trisomies, heartdisease, single gene diseases, HLA typing, phenylketonuria, sickle cellanemia, Tay-Sachs Syndrome, thalassemia, Klinefelter's Syndrome,Huntington's Disease, autoimmune diseases, lipidosis, obesity defects,hemophilia, inborn errors in metabolism, and diabetes.

Cancers which can be detected by the process of the present inventiongenerally involve oncogenes, tumor suppressor genes, or genes involvedin DNA amplification, replication, recombination, or repair. Examples ofthese include: BRCA1 gene, p53 gene, Familial polyposis coli, Her2/Neuamplification, Bcr/Abl, K-ras gene, human papillomavirus Types 16 and18, leukemia, colon cancer, breast cancer, lung cancer, prostate cancer,brain tumors, central nervous system tumors, bladder tumors, melanomas,liver cancer, osteosarcoma and other bone cancers, testicular andovarian carcinomas, ENT tumors, and loss of heterozygosity.

In the area of environmental monitoring, the present invention can beused for detection, identification, and monitoring of pathogenic andindigenous microorganisms in natural and engineered ecosystems andmicrocosms such as in municipal waste water purification systems andwater reservoirs or in polluted areas undergoing bioremediation. It isalso possible to detect plasmids containing genes that can metabolizexenobiotics, to monitor specific target microorganisms in populationdynamic studies, or either to detect, identify, or monitor geneticallymodified microorganisms in the environment and in industrial plants.

The present invention can also be used in a variety or forensic areas,including for human identification for military personnel and criminalinvestigation, paternity testing and family relation analysis, HLAcompatibility typing, and screening blood, sperm, or transplantationorgans for contamination.

In the food and feed industry, the present invention has a wide varietyof applications. For example, it can be used for identification andcharacterization of production organisms such as yeast for production ofbeer, wine, cheese, yogurt, bread, etc. Another area of use is withregard to quality control and certification of products and processes(e.g., livestock, pasteurization, and meat processing) for contaminants.Other uses include the characterization of plants, bulbs, and seeds forbreeding purposes, identification of the presence of plant-specificpathogens, and detection and identification of veterinary infections.

Desirably, the oligonucleotide probes are suitable for ligation togetherat a ligation junction when hybridized adjacent to one another on acorresponding target nucleotide sequence due to perfect complementarityat the ligation junction. However, when the oligonucleotide probes inthe set are hybridized to any other nucleotide sequence present in thesample, there is a mismatch at a base at the ligation junction whichinterferes with ligation. Most preferably, the mismatch is at the baseadjacent the 3′ base at the ligation junction. Alternatively, themismatch can be at the bases adjacent to bases at the ligation junction.

The process of the present invention is able to detect the first andsecond nucleotide sequences in the sample in an amount of 100 attomolesto 250 femtomoles. By coupling the LDR step with a primarypolymerase-directed amplification step, the entire process of thepresent invention is able to detect target nucleotide sequences in asample containing as few as a single molecule. Furthermore, PCRamplified products, which often are in the picomole amounts, may easilybe diluted within the above range. The ligase detection reactionachieves a rate of formation of mismatched ligated product sequenceswhich is less than 0.005 of the rate of formation of matched ligatedproduct sequences.

Once the ligation phase of the process is completed, the capture phaseis initiated. During the capture phase of the process, the mixture iscontacted with the solid support at a temperature of 25-90° C.,preferably 60-80° C., and for a time period of 10-180 minutes,preferably up to 60 minutes. Hybridizations may be accelerated orimproved by mixing the ligation mixture during hybridization, or byadding volume exclusion, chaotropic agents, tetramethylammoniumchloride, or N,N,N, Trimethylglycine (Betaine monohydrate). When anarray consists of dozens to hundreds of addresses, it is important thatthe correct ligation products have an opportunity to hybridize to theappropriate address. This may be achieved by the thermal motion ofoligonucleotides at the high temperatures used, by mechanical movementof the fluid in contact with the array surface, or by moving theoligonucleotides across the array by electric fields. Afterhybridization, the array is washed with buffer to remove unhybridizedprobe and optimize detection of captured probe. Alternatively, the arrayis washed sequentially. The specificity of hybridization may be promotedby the addition of non-specific competitor DNA (e.g. herring sperm DNA)and/or the addition of formamide to the hybridization solution. Thestringency of washing may also be augmented by elevating the washingtemperature and/or adding formamide to the wash buffer. FIG. 16 showsthe results of various combinations of the above alterations to standardhybridization and washing conditions.

Preferably, the solid support has a porous surface of a hydrophilicpolymer composed of combinations of acrylamide with functional monomerscontaining carboxylate, aldehyde, or amino groups. This surface isformed by coating the support with a polyacrylamide based gel. Suitableformulations include mixtures of acrylamide/acrylic acid andN,N-dimethylacrylamide/glycerol monomethacrylate. A crosslinker, N,N′-methylenebisacryl-amide, is present at a level less than 50:1,preferably less than 500:1.

One embodiment of masking negative charges during the contacting of thesolid support with the ligation mixture is achieved by using a divalentcation. The divalent cation can be Mg²⁺, Ca²⁺, MN²⁺, or Co²⁺. Typically,masking with the divalent cation is carried out by pre-hydridizing thesolid support with hybridization buffer containing the cation at aminimum concentration of 10 mM for a period of 15 minutes at roomtemperature.

Another embodiment of masking negative charges during the contacting ofthe solid support with the ligation mixtures is achieved by carrying outthe contacting at a pH at or below 6.0. This is effected by adding abuffer to the ligation mixtures before or during contact of it with thesolid support. Suitable buffers include 2-(N-morpholino)ethanesulfonicacid (MES), sodium phosphate, and potassium phosphate.

Another embodiment of masking negative charges during the contacting ofthe solid support with the ligation mixture is achieved by capping freecarboxylic acid groups with a neutralizing agent while preserving thehydrophillicity of the polymer. Suitable neutralizing agents includeethanolamine diethanolamine, propanolamine, dipropanolamine,isopropanolamine, and diisopropanolamine. Typically, masking withneutralizing agents is carried out by activating the carboxylic acidgroups within the solid support with1-[3-dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride andN-hydroxysuccinimide followed by treatment with a solution of theneutralizing agent in a polar aprotic solvent such as chloroform,dichloromethane, or tetrahydrfuran.

By masking the negative charges in accordance with the presentinvention, an enhanced ability to detect the presence of ligated productin the presence of unligated oligonucleotide probes is achieved. Inparticular, the present invention is effective to detect the presence ofligated product in a ratio to unligated oligonucleotide probes of lessthan 1:300, preferably less than 1:900, more preferably less than1:3000, and most preferably less than 1:9000.

In addition, by masking the negative charges in accordance with thepresent invention, an enhanced ability to detect the presence of atarget nucleotide sequence from a non-target nucleotide sequence wherethe target nucleotide sequence differs from a non-target nucleotidesequence by a single base difference is achieved. In particular, thepresent invention is effective to detect target nucleotide sequence in aratio of the target nucleotide sequence to non-target nucleotidesequence of less than 1:20, preferably less than 1:50, more preferablyless than 1:100, most preferably less than 1:200.

It is important to select capture oligonucleotides and addressablenucleotide sequences which will hybridize in a stable fashion. Thisrequires that the oligonucleotide sets and the capture oligonucleotidesbe configured so that the oligonucleotide sets hybridize to the targetnucleotide sequences at a temperature less than that which the captureoligonucleotides hybridize to the addressable array-specific portions.Unless the oligonucleotides are designed in this fashion, false positivesignals may result due to capture of adjacent unreacted oligonucleotidesfrom the same oligonucleotide set which are hybridized to the target.

The detection phase of the process involves scanning and identifying ifligation of particular oligonucleotide sets occurred and correlatingligation to a presence or absence of the target nucleotide sequence inthe test sample. Scanning can be carried out by scanning electronmicroscopy, confocal microscopy, charge-coupled device, scanningtunneling electron microscopy, infrared microscopy, atomic forcemicroscopy, electrical conductance, and fluorescent or phosphor imaging.Correlating is carried out with a computer.

Another aspect of the present invention relates to a method of formingan array of oligonucleotides on a support. This method involvesproviding a support having an array of positions each suitable forattachment of an oligonucleotide. A linker or support (preferablynon-hydrolyzable), suitable for coupling an oligonucleotide to thesupport at each of the array positions, is attached to the solidsupport. An array of oligonucleotides on a solid support is formed by aseries of cycles of activating selected array positions for attachmentof multimer nucleotides and attaching multimer nucleotides at theactivated array positions.

Yet another aspect of the present invention relates to an array ofoligonucleotides on a support per se. The support has an array ofpositions each suitable for an attachment of an oligonucleotide. Alinker or support (preferably non-hydrolyzable), suitable for couplingan oligonucleotide to the support, is attached to the support at each ofthe array positions. An array of oligonucleotides are placed on asupport with at least some of the array positions being occupied byoligonucleotides having greater than sixteen nucleotides.

In the method of forming arrays, multimer oligonucleotides fromdifferent multimer oligonucleotide sets are attached at different arraypositions on a support. As a result, the support has an array ofpositions with different groups of multimer oligonucleotides attached atdifferent positions.

The 1,000 different addresses can be unique capture oligonucleotidesequences (e.g., 24-mer) linked covalently to the target-specificsequence (e.g., approximately 20- to 25-mer) of a LDR oligonucleotideprobe. A capture oligonucleotide probe sequence does not have anyhomology to either the target sequence or to other sequences on genomeswhich may be present in the sample. This oligonucleotide probe is thencaptured by its addressable array-specific portion, a sequencecomplementary to the capture oligonucleotide on the addressable supportarray. The concept is shown in two possible formats, for example, fordetection of the p53 R248 mutation (FIGS. 17A-C).

FIGS. 17A-C show two alternative formats for oligonucleotide probedesign to identify the presence of a germ line mutation in codon 248 ofthe p53 tumor suppressor gene. The wild type sequence codes for arginine(R248), while the cancer mutation codes for tryptophan (R248W). Thebottom part of the diagram is a schematic diagram of the captureoligonucleotide. The thick horizontal line depicts the membrane orsurface containing the addressable array. The thin curved lines indicatea flexible linker arm. The thicker lines indicate a captureoligonucleotide sequence, attached to the solid surface in the C to Ndirection. For illustrative purposes, the capture oligonucleotides aredrawn vertically, making the linker arm in section B appear “stretched”.Since the arm is flexible, the capture oligonucleotide will be able tohybridize 5′ to C and 3′ to N in each case, as dictated by base paircomplementarity. A similar orientation of oligonucleotide hybridizationwould be allowed if the oligonucleotides were attached to the membraneat the N-terminus. In this case, DNA/PNA hybridization would be instandard antiparallel 5′ to 3′ and 3′ to 5′. Other modifiedsugar-phosphate backbones would be used in a similar fashion. FIG. 17Bshows two LDR probes that are designed to discriminate wild type andmutant p53 by containing the discriminating base C or T at the 3′ end.In the presence of the correct target DNA and Tth ligase, thediscriminating probe is covalently attached to a common downstreamoligonucleotide. The downstream oligonucleotide is fluorescentlylabeled. The discriminating oligonucleotides are distinguished by thepresence of unique addressable array-specific portions, Z1 and Z2, ateach of their 5′ ends. A black dot indicates that target dependentligation has taken place. After ligation, oligonucleotide probes may becaptured by their complementary addressable array-specific portions atunique addresses on the array. Both ligated and unreactedoligonucleotide probes are captured by the oligonucleotide array.Unreacted fluorescently labeled common probes and target DNA are thenwashed away at a high temperature (approximately 65° C. to 80° C.) andlow salt. Mutant signal is distinguished by detection of fluorescentsignal at the capture oligonucleotide complementary to addressablearray-specific portion Z1, while wild type signal appears at the captureoligonucleotide complementary to addressable array-specific portion Z2.Heterozygosity is indicated by equal signals at the captureoligonucleotides complementary to addressable array-specific portions Z1and Z2. The signals may be quantified using a fluorescent imager. Thisformat uses a unique address for each allele and may be preferred forachieving very accurate detection of low levels of signal (30 to 100attomoles of LDR product). FIG. 17C shows the discriminating signals maybe quantified using a fluorescent imager. This format uses a uniqueaddress where oligonucleotide probes are distinguished by havingdifferent fluorescent groups, F1 and F2, on their 5′ end. Eitheroligonucleotide probe may be ligated to a common downstreamoligonucleotide probe containing an addressable array-specific portionZ1 on its 3′ end. In this format, both wild type and mutant LDR productsare captured at the same address on the array, and are distinguished bytheir different fluorescence. This format allows for a more efficientuse of the array and may be preferred when trying to detect hundreds ofpotential germline mutations.

The support can be made from a wide variety of materials. The substratemay be biological, nonbiological, organic, inorganic, or a combinationof any of these, existing as particles, strands, precipitates, gels,sheets, tubing, spheres, containers, capillaries, pads, slices, films,plates, slides, discs, membranes, etc. The substrate may have anyconvenient shape, such as a disc, square, circle, etc. The substrate ispreferably flat but may take on a variety of alternative surfaceconfigurations. For example, the substrate may contain raised ordepressed regions on which the synthesis takes place. The substrate andits surface preferably form a rigid support on which to carry out thereactions described herein. The substrate and its surface is also chosento provide appropriate light-absorbing characteristics. For instance,the substrate may be a polymerized Langmuir Blodgett film,functionalized glass, Si, Ge, GaAs, GaP, SiO₂, SiN₄, modified silicon,or any one of a wide variety of gels or polymers such as(poly)tetrafluoroethylene, (poly)vinylidenedifluoride, polystyrene,polycarbonate, polyethylene, polypropylene, polyvinyl chloride,poly(methyl acrylate), poly(methyl methacrylate), or combinationsthereof. Other substrate materials will be readily apparent to those ofordinary skill in the art upon review of this disclosure. In a preferredembodiment, the substrate is flat glass or single-crystal silicon.

According to some embodiments, the surface of the substrate is etchedusing well known techniques to provide for desired surface features. Forexample, by way of the formation of trenches, v-grooves, mesastructures, raised platforms, or the like, the synthesis regions may bemore closely placed within the focus point of impinging light, beprovided with reflective “mirror” structures for maximization of lightcollection from fluorescent sources, or the like.

Surfaces on the substrate will usually, though not always, be composedof the same material as the substrate. Thus, the surface may be composedof any of a wide variety of materials, for example, polymers, plastics,ceramics, polysaccharides, silica or silica-based materials, carbon,metals, inorganic glasses, membranes, or composites thereof. The surfaceis functionalized with binding members which are attached firmly to thesurface of the substrate. Preferably, the surface functionalities willbe reactive groups such as silanol, olefin, amino, hydroxyl, aldehyde,keto, halo, acyl halide, or carboxyl groups. In some cases, suchfunctionalities preexist on the substrate. For example, silica basedmaterials have silanol groups, polysaccharides have hydroxyl groups, andsynthetic polymers can contain a broad range of functional groups,depending on which monomers they are produced from. Alternatively, ifthe substrate does not contain the desired functional groups, suchgroups can be coupled onto the substrate in one or more steps.

A variety of commercially-available materials, which include suitablymodified glass, plastic, or carbohydrate surfaces or a variety ofmembranes, can be used. Depending on the material, surface functionalgroups (e.g., silanol, hydroxyl, carboxyl, amino) may be present fromthe outset (perhaps as part of the coating polymer), or will require aseparate procedure (e.g., plasma amination, chromic acid oxidation,treatment with a functionalized side chain alkyltrichlorosilane) forintroduction of the functional group. Hydroxyl groups becomeincorporated into stable carbamate (urethane) linkages by severalmethods. Amino functions can be acylated directly, whereas carboxylgroups are activated, e.g., with N,N′-carbonyldiimidazole orwater-soluble carbodiimides, and reacted with an amino-functionalizedcompound. As shown in FIG. 18, the supports can be membranes or surfaceswith a starting functional group X. Functional group transformations canbe carried out in a variety of ways (as needed) to provide group X*which represents one partner in the covalent linkage with group Y*. FIG.18 shows specifically the grafting of PEG (i.e. polyethylene glycol),but the same repertoire of reactions can be used (however needed) toattach carbohydrates (with hydroxyl), linkers (with carboxyl), and/oroligonucleotides that have been extended by suitable functional groups(amino or carboxyl). In some cases, group X* or Y* is pre-activated(isolatable species from a separate reaction); alternatively, activationoccurs in situ. Referring to PEG as drawn in FIG. 18, Y and Y* can bethe same (homobifunctional) or different (heterobifunctional); in thelatter case, Y can be protected for further control of the chemistry.Unreacted amino groups will be blocked by acetylation or succinylation,to ensure a neutral or negatively charged environment that “repels”excess unhybridized DNA. Loading levels can be determined by standardanalytical methods. Fields, et al., “Principles and Practice ofSolid-Phase Peptide Synthesis,” Synthetic Peptides: A User's Guide, G.Grant, Editor, W.H. Freeman and Co.: New York. p. 77-183 (1992), whichis hereby incorporated by reference.

One approach to applying functional groups on a silica-based supportsurface is to silanize with a molecule either having the desiredfunctional group (e.g., olefin, amino, hydroxyl, aldehyde, keto, halo,acyl halide, or carboxyl) or a molecule A able to be coupled to anothermolecule B containing the desired functional group. In the former case,functionalizing of glass- or silica-based supports with, for example, anamino group is carried out by reacting with an amine compound such as3-aminopropyl triethoxysilane, 3-aminopropylmethyldiethoxysilane,3-aminopropyl dimethylethoxysilane, 3-aminopropyl trimethoxysilane,N-(2-aminoethyl)-3-aminopropylmethyl dimethoxysilane,N-(2-aminoethyl-3-aminopropyl) trimethoxysilane, aminophenyltrimethoxysilane, 4-aminobutyldimethyl methoxysilane, 4-aminobutyltriethoxysilane, aminoethylaminomethyphenethyl trimethoxysilane, ormixtures thereof. In the latter case, molecule A preferably containsolefinic groups, such as vinyl, acrylate, methacrylate, or allyl, whilemolecule B contains olefinic groups and the desired functional groups.In this case, molecules A and B are polymerized together. In some cases,it is desirable to modify the silanized surface to modify its properties(e.g., to impart biocompatibility and to increase mechanical stability).This can be achieved by addition of olefinic molecule C along withmolecule B to produce a polymer network containing molecules A, B, andC.

Molecule A is defined by the following formula:

R¹ is H or CH₃

R² is (C═O)—O—R⁶, aliphatic group with or without functionalsubstituent(s), an aromatic group with or without functionalsubstituent(s), or mixed aliphatic/aromatic groups with or withoutfunctional substituent(s);

R³ is an O-alkyl, alkyl, or halogen group;

R⁴ is an O-alkyl, alkyl, or halogen group;

R⁵ is an O-alkyl, alkyl, or halogen group; and

R⁶ is an aliphatic group with or without functional substituent(s), anaromatic group with or without functional substituent(s), or mixedaliphatic/aromatic groups with or without functional substituent(s).Examples of Molecule A include 3-(trimethoxysilyl)propyl methacrylate,N-[3-(trimethoxysilyl)propyl]-N′-(4-vinylbenzyl)ethylenediamine,triethoxyvinylsilane, triethylvinylsilane, vinyltrichlorosilane,vinyltrimethoxysilane, and vinylytrimethylsilane.

Molecule B can be any monomer containing one or more of the functionalgroups described above. Molecule B is defined by the following formula:

(i) R¹ is H or CH₃,

R² is (C═O), and

R³ is OH or Cl.

or

(ii) R¹ is H or CH₃ and

R² is (C═O)—O—R⁴, an aliphatic group with or without functionalsubstituent(s), an aromatic group with or without functionalsubstituent(s), and mixed aliphatic/aromatic groups with or withoutfunctional substituent(s); and

R³ is a functional group, such as OH, COOH, NH₂, halogen, SH, COCl, oractive ester; and

R⁴ is an aliphatic group with or without functional substituent(s), anaromatic group with or without functional substituent(s), or mixedaliphatic/aromatic groups with or without functional substituent(s).Examples of molecule B include acrylic acid, acrylamide, methacrylicacid, vinylacetic acid, 4-vinylbenzoic acid, itaconic acid, allyl amine,allylethylamine, 4-aminostyrene, 2-aminoethyl methacrylate, acryloylchloride, methacryloyl chloride, chlorostyrene, dichlorostyrene,4-hydroxystyrene, hydroxymethyl styrene, vinylbenzyl alcohol, allylalcohol, 2-hydroxyethyl methacrylate, or poly(ethylene glycol)methacrylate.

Molecule C can be any molecule capable of polymerizing to molecule A,molecule B, or both and may optionally contain one or more of thefunctional groups described above. Molecule C can be any monomer orcross-linker, such as acrylic acid, methacrylic acid, vinylacetic acid,4-vinylbenzoic acid, itaconic acid, allyl amine, allylethylamine,4-aminostyrene, 2-aminoethyl methacrylate, acryloyl chloride,methacryloyl chloride, chlorostyrene, dichlorostyrene, 4-hydroxystyrene,hydroxymethyl styrene, vinylbenzyl alcohol, allyl alcohol,2-hydroxyethyl methacrylate, poly(ethylene glycol) methacrylate, methylacrylate, methyl methacrylate, ethyl acrylate, ethyl methacrylate,styrene, 1-vinylimidazole, 2-vinylpyridine, 4-vinylpyridine,divinylbenzene, ethylene glycol dimethacryarylate,N,N′-methylenediacrylamide, N,N′-phenylenediacrylamide,3,5-bis(acryloylamido)benzoic acid, pentaerythritol triacrylate,trimethylolpropane trimethacrylate, pentaerythritol tetraacrylate,trimethylolpropane ethoxylate (14/3 EO/OH) triacrylate,trimethyolpropane ethoxylate (7/3 EO/OH) triacrylate, triethylolpropanepropoxylate (1 PO/OH) triacrylate, or trimethyolpropane propoxylate (2PO/PH triacrylate).

Generally, the functional groups serve as starting points foroligonucleotides that will ultimately be coupled to the support. Thesefunctional groups can be reactive with an organic group that is to beattached to the support or it can be modified to be reactive with thatgroup, as through the use of linkers or handles. The functional groupscan also impart various desired properties to the support.

After functionalization (if necessary) of the support, tailor-madepolymer networks containing activated functional groups that may serveas carrier sites for complementary oligonucleotide capture probes can begrafted to the support. The advantage of this approach is that theloading capacity of capture probes can thus be increased significantly,while physical properties of the intermediate solid-to-liquid phase canbe controlled better. Parameters that are subject to optimizationinclude the type and concentration of functional group-containingmonomers, as well as the type and relative concentration of thecrosslinkers that are used.

The surface of the functionalized substrate is preferably provided witha layer of linker molecules, although it will be understood that thelinker molecules are not required elements of the invention. The linkermolecules are preferably of sufficient length to permit polymers in acompleted substrate to interact freely with molecules exposed to thesubstrate. The linker molecules should be 6-50 atoms long to providesufficient exposure. The linker molecules may be, for example, arylacetylene, ethylene glycol oligomers containing 2-10 monomer units,diamines, diacids, amino acids, or combinations thereof.

According to alternative embodiments, the linker molecules are selectedbased upon their hydrophilic/hydrophobic properties to improvepresentation of synthesized polymers to certain receptors. For example,in the case of a hydrophilic receptor, hydrophilic linker molecules willbe preferred to permit the receptor to approach more closely thesynthesized polymer.

According to another alternative embodiment, linker molecules are alsoprovided with a photocleavable group at any intermediate position. Thephotocleavable group is preferably cleavable at a wavelength differentfrom the protective group. This enables removal of the various polymersfollowing completion of the syntheses by way of exposure to thedifferent wavelengths of light.

The linker molecules can be attached to the substrate via carbon-carbonbonds using, for example, (poly)tri-fluorochloroethylene surfaces or,preferably, by siloxane bonds (using, for example, glass or siliconoxide surfaces). Siloxane bonds with the surface of the substrate may beformed in one embodiment via reactions of linker molecules bearingtrichlorosilyl groups. The linker molecules may optionally be attachedin an ordered array, i.e., as parts of the head groups in a polymerizedmonolayer. In alternative embodiments, the linker molecules are adsorbedto the surface of the substrate.

As an example of assembling arrays with multimers, such assembly can beachieved with tetramers. Of the 256 (4⁴) possible ways in which fourbases can be arranged as tetramers, 36 that have unique sequences can beselected. Each of the chosen tetramers differs from all the others by atleast two bases, and no two dimers are complementary to each other.Furthermore, tetramers that would result in self-pairing or hairpinformation of the addresses have been eliminated.

The final tetramers are listed in Table 1 and have been numberedarbitrarily from 1 to 36. This unique set of tetramers are used asdesign modules for the sometimes desired 24-mer capture oligonucleotideaddress sequences. The structures can be assembled by stepwise (one baseat a time) or convergent (tetramer building blocks) syntheticstrategies. Many other sets of tetramers may be designed which followthe above rules. The segment approach is not uniquely limited totetramers, and other units, i.e. dimers, trimers, pentamers, or hexamerscould also be used.

TABLE 1 List of tetramer PNA sequences and complementaryDNA sequences, which differ from each other by at least 2 bases. NumberSequence (N-C) Complement (5′-3′) G + C 1. TCTG CAGA 2 2. TGTC GACA 2 3.TCCC GGGA 3 4. TGCG CGCA 3 5. TCGT ACGA 2 6. TTGA TCAA 1 7. TGAT ATCA 18. TTAG CTAA 1 9. CTTG CAAG 2 10. CGTT AACG 2 11. CTCA TGAG 2 12. CACGCGTG 3 13. CTGT ACAG 2 14. CAGC GCTG 3 15. CCAT ATGG 2 16. CGAA TTCG 217. GCTT AAGC 2 18. GGTA TACC 2 19. GTCT AGAC 2 20. GACC GGTC 3 21. GAGTACTC 2 22. GTGC GCAC 3 23. GCAA TTGC 2 24. GGAC GTCC 3 25. AGTG CACT 226. AATC GATT 1 27. ACCT AGGT 2 28. ATCG CGAT 2 29. ACGG CCGT 3 30. AGGATCCT 2 31. ATAC GTAT 1 32. AAAG CTTT 1 33. CCTA TAGG 2 34. GATG CATC 235. AGCC GGCT 3 36. TACA TGTA 1Note that the numbering scheme for tetramers permits abbreviation ofeach address as a string of six numbers (e.g., second column of Table 2infra). The concept of a 24-mer address designed from a unique set of 36tetramers (Table 1) allows a huge number of possible structures,36⁶=2,176,782,336.

FIG. 19 shows one of the many possible designs of 36 tetramers whichdiffer from each other by at least 2 bases. The checkerboard patternshows all 256 possible tetramers. A given square represents the firsttwo bases on the left followed by the two bases on the top of thecheckerboard. Each tetramer must differ from each other by at least twobases, and should be non-complementary. The tetramers are shown in thewhite boxes, while their complements are listed as (number). Thus, thecomplementary sequences GACC (20) and GGTC (20′) are mutually exclusivein this scheme. In addition, tetramers must be non-palindromic, e.g.,TCGA (darker diagonal line boxes), and non-repetitive, e.g., CACA(darker diagonal line boxes from upper left to lower right). All othersequences which differ from the 36 tetramers by only 1 base are shadedin light gray. Four potential tetramers (white box) were not chosen asthey are either all A•T or G•C bases. However, as shown below, the T_(m)values of A•T bases can be raised to almost the level of G•C bases.Thus, all A•T or G•C base tetramers (including the ones in white boxes)could potentially be used in a tetramer design. In addition, thymine canbe replaced by 5-propynyl uridine when used within captureoligonucleotide address sequences as well as in the oligonucleotideprobe addressable array-specific portions. This would increase the T_(m)of an A•T base pair by •1.7° C. Thus, T_(m) values of individualtetramers should be approximately 15.1° C. to 15.7° C. T_(m) values forthe full length 24-mers should be 95° C. or higher.

To illustrate the concept, a subset of six of the 36 tetramer sequenceswere used to construct arrays: 1=TGCG; 2=ATCG; 3=CAGC; 4=GGTA; 5=GACC;and 6=ACCT. This unique set of tetramers can be used as design modulesfor the required 24-mer addressable array-specific portion and 24-mercomplementary capture oligonucleotide address sequences. This embodimentinvolves synthesis of five addressable array-specific portion (sequenceslisted in Table 2). Note that the numbering scheme for tetramers allowsabbreviation of each portion (referred to as “Zip #”) as a string of sixnumbers (referred to as “zip code”).

TABLE 2 List of all 5 DNA/PNA oligonucleotide address sequences.Sequence (5′ → 3′ or G + Zip # Zip code NH₂ → COOH) C Zip11 1-4-3-6-6-1TGCG-GGTA-CAGC-ACCT-ACCT-TGCG 15 (SEQ ID NO: 9268) Zip12 2-4-4-6-1-1ATCG-GGTA-GGTA-ACCT-TGCG-TGCG 14 (SEQ ID NO: 9269) Zip13 3-4-5-6-2-1CAGC-GGTA-GACC-ACCT-ATCG-TGCG 15 (SEQ ID NO: 9270) Zip14 4-4-6-6-3-1GGTA-GGTA-ACCT-ACCT-CAGC-TGCG 14 (SEQ ID NO: 9271) Zip15 5-4-1-6-4-1GACC-GGTA-TGCG-ACCT-GGTA-TGCG 15 (SEQ ID NO: 9272)Each of these oligomers contains a hexaethylene oxide linker arm ontheir 5′ termini [P. Grossman, et al., Nucl. Acids Res., 22:4527-4534(1994), which is hereby incorporated by reference], and ultimateamino-functions suitable for attachment onto the surfaces of glassslides, or alternative materials. Conjugation methods will depend on thefree surface functional groups [Y. Zhang, et al., Nucleic Acids Res.,19:3929-3933 (1991) and Z. Guo, et al., Nucleic Acids Res., 34:5456-5465(1994), which are hereby incorporated by reference].

Synthetic oligonucleotides (normal and complementary directions, eitherfor capture hybridization or hybridization/ligation) are prepared aseither DNA or PNA, with either natural bases or nucleotide analogues.Such analogues pair with perfect complementarity to the natural basesbut increase T_(m) values (e.g., 5-propynyl-uracil).

In accordance with the present invention, false hybridization signalsfrom DNA synthesis errors are avoided. Addresses can be designed sothere are very large differences in hybridization T_(m) values toincorrect address. In contrast, the direct hybridization approachesdepend on subtle differences. The present invention also eliminatesproblems of false data interpretation with gel electrophoresis orcapillary electrophoresis resulting from either DNA synthesis errors,band broadening, or false band migration.

The use of a capture oligonucleotide to detect the presence of ligationproducts, eliminates the need to detect single-base differences inoligonucleotides using differential hybridization. Other existingmethods in the prior art relying on allele-specific PCR, differentialhybridization, or sequencing-by-hybridization methods must havehybridization conditions optimized individually for each new sequencebeing analyzed. When attempting to detect multiple mutationssimultaneously, it becomes difficult or impossible to optimizehybridization conditions. In contrast, the present invention is ageneral method for high specificity detection of correct signal,independent of the target sequence, and under uniform hybridizationconditions. The present invention yields a flexible method fordiscriminating between different oligonucleotide sequences withsignificantly greater fidelity than by any methods currently availablewithin the prior art.

The array of the present invention will be universal, making it usefulfor detection of cancer mutations, inherited (germline) mutations, andinfectious diseases. Further benefit is obtained from being able toreuse the array, lowering the cost per sample.

The present invention also affords great flexibility in the synthesis ofoligonucleotides and their attachment to supports. Oligonucleotides canbe synthesized off of the support and then attached to unique surfaceson the support. Segments of multimers of oligonucleotides, which do notrequire intermediate backbone protection (e.g., PNA), can be synthesizedand linked onto to the solid support. Added benefit is achieved by beingable to integrate these synthetic approaches with design of the captureoligonucleotide addresses. Such production of solid supports is amenableto automated manufacture, obviating the need for human intervention andresulting contamination concerns.

An important advantage of the array of the present invention is theability to reuse it with the previously attached captureoligonucleotides. In order to prepare the solid support for such reuse,the captured oligonucleotides must be removed without removing thelinking components connecting the captured oligonucleotides to the solidsupport. A variety of procedures can be used to achieve this objective.For example, the solid support can be treated in distilled water at95-100° C., subjected to 0.01 N NaOH at room temperature, contacted with50% dimethylformamide at 90-95° C., or treated with 50% formamide at90-95° C. Generally, this procedure can be used to remove capturedoligonucleotides in about 5 minutes. These conditions are suitable fordisrupting DNA-DNA hybridizations; DNA-PNA hybridizations require otherdisrupting conditions.

The present invention is illustrated, but not limited, by the followingexamples.

EXAMPLES Example 1—Materials and Methods

Oligonucleotide Synthesis and Purification.

Oligonucleotides were obtained as custom synthesis products from IDT,Inc. (Coralville, Iowa), or synthesized in-house on an ABI 394 DNASynthesizer (PE Biosystems Inc.; Foster City, Calif.) using standardphosphoramidite chemistry. Spacer phosphoramidite 18, 3′-amino-modiferC3 CPG, and 3′-fluorescein CPG were purchased from Glen Research(Sterling, Va.). All other reagents were purchased from PE Biosystems.Both labeled and unlabeled oligonucleotides were purified byelectrophoresis on 12% denaturing polyacrylamide gels. Bands werevisualized by UV shadowing, excised from the gel, and eluted overnightin 0.5 M NaCl, 5 mM EDTA, pH 8.0 at 37° C. Oligonucleotide solutionswere desalted on C18 Sep-Pak® separation columns (Waters Corporation;Milford, Mass.) according to the manufacturer's instructions, followingwhich the oligonucleotides were concentrated to dryness (Speed-Vac) andstored at −20° C.

Cleaning of Microscope Slides.

Glass microscope slides (VWR, precleaned, 3 in.×1 in.×1.2 mm) wereincubated in boiling conc. NH₄OH—30% H₂O₂—H₂O (1:1:5, v/v/v) for 10 minand rinsed in distilled water. A second incubation was performed inboiling conc. HCl—30% H₂O₂—H₂O for 10 min. See U. Jonsson, et al.,“Absorption Behavior of Fibronetin on Well Characterized SilicaSurfaces,” J. Colloid Interface Sci. 90:148-163 (1982), which is herebyincorporated by reference. The slides were rinsed thoroughly indistilled water, methanol, and acetone, and were air-dried at room temp.

Polymer Coated Slides.

Immediately following cleaning, slides (Fisher Scientific, precleaned, 3in.×1 in.×1.2 mm) were immersed in 2%methacryloxypropyltrimethoxysilane, 0.2% triethylamine in CHCl₃ for 30min at 25° C., and then washed with CHCl₃ (2×15 min). A monomer solution[20 μL: 8% acrylamide, 2% acrylic acid, 0.02%N,N′-methylene-bisacrylamide (500:1 ratio of monomers:crosslinker), 0.8%ammonium persulfate radical polymerization initiator] was deposited onone end of the slides and spread out with the aid of a cover slip (24×50mm) that had been previously silanized [5% (CH₃)₂SiCl₂ in CHCl₃].Polymerization was achieved by heating the slides on a 70° C. hot platefor 4.5 min. Upon removal of the slides from the hot plate, the coverslips were immediately peeled off with aid of a single-edge razor blade.The coated slides were rinsed with deionized water, allowed to dry in anopen atmosphere, and stored under ambient conditions.

Preparation of Zip-Code Arrays.

Polymer-coated slides were pre-activated by immersing them for 30 min at25° C. in a solution of 0.1 M1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride plus 20 mMN-hydroxysuccinimide in 0.1 M K₂HPO₄/KH₂PO₄, pH 6.0. The activatedslides were rinsed with water, and then dried in a 65° C. oven; theywere stable upon storage for 6 months or longer at 25° C. in adesiccator over Drierite.

Arrays were spotted on a Cartesian Technologies Pixsys 5500 robot at 25°C. and 70% relative humidity using 500 μM zip-code oligonucleotidesolutions in 0.2 M K₂HPO₄/KH₂PO₄, pH 8.3. Each address was spotted inquadruplicate. Additionally, Cy3, Cy5, and fluorescein fiducials wereprinted along the top and down the right hand side of each array.Following spotting, uncoupled oligonucleotides were removed from thepolymer surfaces by soaking the slides in 300 mM bicine, pH 8.0, 300 mMNaCl, 0.1% SDS, for 30 min at 65° C., rinsing with water, and drying.The arrays were stored at 25° C. in slide boxes until needed.

PCR Amplification of K-Ras DNA Samples.

PCR amplifications were carried out under paraffin oil in 50 μL reactionmixtures containing 10 mM Tris•HCl, pH 8.3, 4 mM MgCl₂, 50 mM KCl, 800μM dNTPs, 1 μM forward and reverse primers (50 pmol of each primer;K-rasEx1forward and K-rasEx1reverse (Table 3)), 1 U AmpliTaq Gold, and100 ng of genomic DNA extracted from paraffin-embedded tumors or fromcell lines. Reactions were preincubated for 10 min at 95° C.Amplification was achieved by thermally cycling for 40 rounds of 94° C.for 30 sec; 60° C. for 1 min; and 72° C. for 1 min, followed by a finalelongation at 72° C. for 5 min. Following PCR, 1 μL of Proteinase K (18mg/mL) was added, and reactions were heated to 70° C. for 10 min andthen quenched at 95° C. for 15 min. Two μL of each PCR product wasanalyzed on a 3% agarose gel to verify the presence of amplificationproduct of the expected size.

LDR of K-ras DNA samples. LDR was carried out under paraffin oil in 20μL volumes containing 20 mM Tris•HCl, pH 8.5-5 mM MgCl₂—100 mM KCl, 10mM DTT, 1 mM NAD⁺, 10 pmol total LDR probes [500 fmol each offluorescently-labeled discriminating probes (K-rasc32Wt, labeled withCy3, Cy5, and fluorescein; K-rasc12.2D labeled with Cy3; K-rasc12.2Alabeled with Cy5; K-rasc12.2V labeled with fluorescein; K-rasc12.1Slabeled with Cy3; K-rasc12.1R, labeled with Cy5; K-rasc12.1C, labeledwith fluorescein; and K-rasc13.4D labeled with Cy3)+5 pmol total commonprobes; (1500 fmol each of K-rascd32Com9cZip1, K-rascd12Com2cZip2, andK-rascd12Com1cZip3, and 500 fmol of K-rascd13Com4cZip4) (Table 3)], and2 μL PCR products from the cell line or tumor samples. The reactionmixtures were pre-heated for 2 min at 94° C., and then 25 fmol ofwild-type Tth DNA ligase was added. The LDR reaction mixtures werecycled for 20 rounds of 94° C. for 30 sec and 65° C. for 4 min.

Hybridization of K-Ras LDR Products to DNA Arrays.

The LDR reaction mixtures were diluted with 20 μL of 2× hybridizationbuffer to produce a final buffer concentration of 300 mM MES, pH 6.0, 10mM MgCl₂, 0.1% SDS, denatured at 94° C. for 3 min, and chilled on ice.Arrays were pre-incubated for 15 min at 25° C. in 1× hybridizationbuffer. Coverwells (Grace, Inc; Sunriver, Oreg.) were attached to thearrays and filled with 30 μL of the diluted LDR reaction mixtures. Thearrays were placed in humidified culture tubes and incubated for 1 h at65° C. and 20 rpm in a rotating hybridization oven. Followinghybridization, the arrays were washed in 300 mM bicine, pH 8.0, 10 mMMgCl₂, 0.1% SDS for 10 min at 25° C. Fluorescent signals were measuredusing a Scanarray 5000 (GSI Lumonics).

LDR detection of 7 specific mutations in K-ras on an addressableuniversal microarray is shown in FIG. 36. The three signals along thetop and those down the right hand side of each array are fiducials usedfor alignment. The next 4 addresses across in the second row correspondto addresses #1, #2, #3, and #4, complements of cZip1, cZip2, cZip3, andcZip4, respectively. The eight cell line (i.e. COL0205, LS180, SW1116,SW480, and DLD1) and tumor samples (G12S, G12R, and G12C) correctlyidentified the mutations present. Wild-type cell line COL0205 gave Cy3,Cy5, and fluorescein signal at address #1. The wild-type signal ataddress #1 was used as a control for all experiments. The LS180 cellline containing the Asp12 mutation gave a Cy3 signal at address #2. TheSW1116 cell line containing the Ala12 mutation gave a Cy5 signal ataddress #2. The SW480 cell line containing the Val12 mutation gave afluorescein signal at address #2. The G12S tumor sample containing theSer12 mutation gave a Cy3 signal at address #3. The G12R tumor samplecontaining the Arg12 mutation gave a Cy5 signal at address #3. The G12Ctumor sample containing the Cys12 mutation gave a fluorescein signal ataddress #3. The DLD1 cell line containing the Asp13 mutation gave a Cy3signal at address #4. The incorrect signals seen at Zip4 in the LS180and SW1116 samples were due to contamination of the samples.

TABLE 3Primers designed for mutation detection in K-ras by PCR/LDR/ArrayHybridization. Primer Sequence (5′→3′) K-rasEx1forwardAAC CTT ATG TGT GAC ATG TTC TAA TAT AGT CAC (SEQ ID NO: 9273)K-rasEx1reverseAAA ATG GTC AGA GAA ACC TTT ATC TGT ATC (SEQ ID NO: 9274)K-rascd32Com9cZip1 PTATGATCCAACAATAGAGGTAAATCTTGTCGCAGATTTTGCGCTGGATTTCAA (SEQ ID NO: 9275) K-rasc32WtCy3-ATTCAGAATCATTTTGTGGACGAA (SEQ ID NO: 9276)Cy5-ATTCAGAATCATTTTGTGGACGAA (SEQ ID NO: 9276)Fam-ATTCAGAATCATTTTGTGGACGAA (SEQ ID NO: 9276) K-rascd12Com2cZip2PTGGCGTAGGCAAGAGTGCCTTTCGCCGTCGTGTAGGCTTTTCAA (SEQ ID NO: 9277)K-rasc12.2D Cy3-AAACTTGTGGTAGTTGGAGCTGA (SEQ ID NO: 9278) K-rasc12.2ACy5-AAACTTGTGGTAGTTGGAGCTGC (SEQ ID NO: 9279) K-rasc12.2VFam-AAACTTGTGGTAGTTGGAGCTGT (SEQ ID NO: 9280) K-rascd12Com1cZip3PGTGGCGTAGGCAAGAGTGCCCCGTAAGCCCGTATGGCAGATCAA (SEQ ID NO: 9281)K-rasc12.1S Cy3-ATATAAACTTGTGGTAGTTGGAGCTA (SEQ ID NO: 9282) K-rasc12.1RCy5-ATATAAACTTGTGGTAGTTGGAGCTC (SEQ ID NO: 9283) K-rasc12.1CFam-ATATAAACTTGTGGTAGTTGGAGCTT (SEQ ID NO: 9284) K-rascd13 Com4cZip4PCGTAGGCAAGAGTGCCTTGACATGGCCGTGCTGGGGACA AGTCAA (SEQ ID NO: 9285)K-rasc13.4D Cy3-TGTGGTAGTTGGAGCTGGTGA (SEQ ID NO: 9286)Amplification was achieved by thermal cycling for 40 rounds of 94° C.for 15 sec and 60° C. for 2 min, followed by a final elongation step at65° C. for 5 min. Following PCR, 1 μL of Proteinase K (18 mg/mL) wasadded, and reactions were heated to 70° C. for 10 min and then quenchedat 95° C. for 15 min. One μL of each PCR product was analyzed on a 3%agarose gel to verify the presence of amplification product of theexpected size.

LDR of K-ras DNA samples. LDR reactions were carried out under paraffinoil in 20 μL volumes containing 20 mM Tris•HCl, pH 8.5, 5 mM MgCl₂, 100mM KCl, 10 mM DTT, 1 mM NAD⁺, 8 pmol total LDR probes (500 fmol each ofdiscriminating probes+4 pmol fluorescently-labeled common probes), and 1pmol PCR products from cell line or tumor samples. Two probe mixes wereprepared, each containing the seven mutation-specific probes, the threecommon probes, and either the wild-type discriminating probe for codon12 or that for codon 13 (Table 3).

The reaction mixtures were pre-heated for 2 min at 94° C., and then 25fmol of wild-type Tth DNA ligase was added. The LDR reactions werecycled for 20 rounds of 94° C. for 15 sec and 65° C. for 4 min. Analiquot of 2 μL of each reaction was mixed with 2 L of gel loadingbuffer [8% blue dextran, 50 mM EDTA, pH 8.0-formamide (1:5)], denaturedat 94° C. for 2 min, and chilled on ice. One μL of each mixture wasloaded on a 10% denaturing polyacrylamide gel and electrophoresed on anABI 377 DNA sequencer at 1500 volts.

Hybridization of K-Ras LDR Products to DNA Arrays.

The LDR reactions (17 μL) were diluted with 40 μL of 1.4× hybridizationbuffer to produce a final buffer concentration of 300 mM MES, pH 6.0, 10mM MgCl₂, 0.1% SDS. Arrays were pre-incubated for 15 min at 25° C. in 1×hybridization buffer. Coverwells (Grace, Inc; Sunriver, Oreg.) werefilled with the diluted LDR reactions and attached to the arrays. Thearrays were placed in humidified culture tubes and incubated for 1 h at65° C. and 20 rpm in a rotating hybridization oven. Followinghybridization, the arrays were washed in 300 mM bicine, pH 8.0, 10 mMMgCl₂, 0.1% SDS for 10 min at 25° C. Fluorescent signals were measuredusing a microscope/CCD, as described in the following paragraph.

Image Analysis.

Arrays were imaged using a Molecular Dynamics Fluorlmager™ 595dual-excitation, laser induced fluorescence scanner (Sunnyvale, Calif.)or an Olympus AX70 epifluorescence microscope (Melville, N.Y.) equippedwith a Princeton Instruments TE/CCD-512 TKBM1 camera (Trenton, N.J.).For analysis of fluorescein-labeled probes on the Fluorlmager™ 595dual-excitation, laser induced fluorescence scanner the 488 nmexcitation was used with a 530/30 emission filter. The spatialresolution of scans was 100 μm per pixel. The resulting images wereanalyzed using ImageQuaNT™ software provided with the instrument. Theepifluorescence microscope was equipped with a 100 W mercury lamp, aFITC filter cube (excitation 480/40, dichroic beam splitter 505,emission 535/50), a Texas Red filter cube (excitation 560/55, dichroicbeam splitter 595, emission 645/75), and a 100 mm macro objective. Themacro objective allows illumination of an object field up to 15 mm indiameter and projects a 7×7 mm area of the array onto the 12.3×12.3 mmmatrix of the CCD. Images were collected in 16-bit mode using theWinview32 software provided with the camera. Analysis was performedusing Scion Image imaging software (Scion Corporation, Frederick, Md.).

Example 2—Amplification of BRCA1 and BRCA2 Exons for PCR/PCR/LDRDetection of Wild-Type and Mutant Alleles

A multiplex assay was used to detect small insertions and deletionsusing a modified PCR to evenly amplify each amplicon (PCR/PCR)(Belgrader et al., “A Multiplex PCR-Ligase Detection Reaction Assay forHuman Identity Testing,” Genome Science and Technology 1:77-87 (1996),which is hereby incorporated by reference) followed by ligase detectionreaction (“LDR”) (Khanna, M. et al., “Multiplex PCR/LDR for Detection ofK-ras Mutations in Primary Colon Tumors,” Oncogene 18:27-38 (1999),which is hereby incorporated by reference). FIG. 20 shows how multiplexamplification of the relevant exons is carried out to ensure equalamplification of all products: a limited number of PCR cycles wasperformed using gene-specific primers, with further rounds ofamplification primed from the universal sequences located at the extreme5′-ends of the PCR primers. This approach minimizes amplification biasdue to primer-specific effects. LDR was next used to detect bothwild-type and mutant versions of the queried sequence. The ligationoligonucleotides probes hybridize to both wild-type and mutant products,but ligate only when both probes are perfectly matched with no gaps oroverlaps. Products can be either eletrophoretically separated orhybridized to a microarray for identification.

PCR was carried out as a single-tube, multiplex reaction in order tosimultaneously amplify BRCA1 exons 2 and 20 and BRCA2 exon 11. GenomicDNA was extracted from blood samples of Ashkenazi Jewish individuals andamplified in a 25 μl reaction mixture containing 100 ng of DNA, 400 μMof each dNTP, 1×PCR Buffer II (10 mM Tris-HCl pH 8.3 at 25° C., 50 mMKCl) supplemented with 4 mM MgCl₂, 1 U AmpliTaq Gold and 2 pmol of eachgene-specific primer bearing either universal primer A or B on the 5′ends. Table 4 shows the primers and probes for detection of BRCA1 andBRCA2 mutations using PCR/LDR/array hybridization as follows:

TABLE 4 Primers and Probes designed for mutation detection in BRCA1 andBRCA2 by PCR/LDR/Array Hybridization. Primer Sequence (5′→3′)PCR primers: Universal primer A (Uni A) 5′ ggagcacgctatcccgttagac 3′(SEQ ID NO: 9287) Universal primer B (Uni B) 5′ cgctgccaactaccgcacatg 3′(SEQ ID NO: 9288) BRCA1 exon 2 forward 5′Uni A - TCATTGGAACAGAAAGAAATGGATTTATC 3′ (SEQ ID NO: 9289)BRCA1 exon 2 reverse 5′ Uni B - TCTTCCCTAGTATGTAAGGTCAATTCTGTTC 3′(SEQ ID NO: 9290) BRCA1 exon 20 forward 5′Uni A - ACTTCCATTGAAGGAAGCTTCTCTTTC 3′ (SEQ ID NO: 9291)BRCA1 exon 20 reverse 5′ Uni B - ATCTCTGCAAAGGGGAGTGGAATAC 3′(SEQ ID NO: 9292) BRCA2 exon 11 forward 5′Uni A - CAAAATATGTCTGGATTGGAGAAAGTTTC 3′ (SEQ ID NO: 9293)BRCA2 exon 11 reverse 5′ Uni B - TTGGAAAAGACTTGCTTGGTACTATCTTC 3′(SEQ ID NO: 9294) LDR Gel-Based Assay:Discriminating Oligonucleotide Probes: BRCA1 ex 2 wild-type position 1855′ Fam - aaCATTAATGCTATGCAGAAAATCTTAGAG 3′ (SEQ ID NO: 9295)BRCA1 ex 2 position 185 del AG mutation 5′Tet - GTCATTAATGCTATGCAGAAAATCTTAG 3′ (SEQ ID NO: 9296)BRCA1 ex 20 wild-type position 5382 5′ Fam - CCAAAGCGAGCAAGAGAATCC 3′(SEQ ID NO: 9297) BRCA1 ex 20 position 5382 ins C mutation 5′Tet - aaCAAAGCGAGCAAGAGAATCCC 3′ (SEQ ID NO: 9298)BRCA2 ex 11 wild-type position 6174 5′Fam - caCTTGTGGGATTTTTAGCACAGCAAGT 3′ (SEQ ID NO: 9299)BRCA2 ex 11 position 6174 del T mutation 5′Tet - TACTTGTGGGATTTTTAGCACAGCAAG 3′ (SEQ ID NO: 9300)LDR Common Oligonucleotide Probes: BRCA1 ex 2 position 185 5′P-TGTCCCATCTGGTAAGTCAGCACAAAC-B 3′ (SEQ ID NO: 9301)BRCA1 ex 20 position 5382 5′ P-CAGGACAGAAAGGTAAAGCTCCCTC-B 3′(SEQ ID NO: 9302) BRCA2 ex 11 position 6174 5′P-GGAAAATCTGTCCAGGTATCAGAT-B 3′ (SEQ ID NO: 9303) LDR Microarray Assay:Discriminating Oligonucleotide Probes: BRCA1 ex 2 control 5′Cy3 - TGCATAGGAGATAATCATAGGAATCC 3′ (SEQ ID NO: 9304)BRCA1 ex 2 position 185 del AG mutation 5′Cy3 - GTCATTAATGCTATGCAGAAAATCTTAG 3′ (SEQ ID NO: 9305)BRCA1 ex 20 control 5′ Cy3 - CCTCTGACTTCAAAATCATGCTG 3′(SEQ ID NO: 9306) BRCA1 ex 20 position 5382 ins C mutation 5′Cy3 - CAAAGCGAGCAAGAGAATCCC 3′ (SEQ ID NO: 9307) BRCA2 ex 11 control 5′Cy3 - CTTCCCTATACTACATTTACATATATCTGAAG 3′ (SEQ ID NO: 9308)BRCA2 ex 11 position 6174 del T mutation 5′Cy3 - TACTTGTGGGATTTTTAGCACAGCAAG 3′ (SEQ ID NO: 9309)Common Oligonucleotide Probes for Controls: BRCA1 exon 2 control +cZip 1 ′ P-CAAATTAATACACTCTTGTGCTGACTTACCA-cgcagattttgcgctggatttcaa-B 3′(SEQ ID NO: 9310) BRCA1 exon 20 control + cZip 2 5′P-AAAGAAACCAAACACAACCCATCAG-ttcgccgtcgtgtaggcttttcaa-B 3′(SEQ ID NO: 9311) BRCA2 exon 11 control + cZip 3 5′P-TTTCCAAACTAACATCACAAGGTGATATTT-ccgtaagcccgtatggcagatcaa-B 3′(SEQ ID NO: 9312) Common Oligonucleotide Probes for Mutations:BRCA1 exon 2 position 185 + cZip 9 5′P-TGTCCCATCTGGTAAGTCAGCACAAAC-catcgtccctttcgatgggatcaa-B 3′(SEQ ID NO: 9313) BRCA1 exon 20 position 5382 + cZip 10 5′P-CAGGACAGAAAGGTAAAGCTCCCTC-caaggcacgtcccagacgcatcaa-B 3′(SEQ ID NO: 9314) BRCA2 exon 11 position 6174 + cZip 11 5′P-GGAAAATCTGTCCAGGTATCAGAT-gcacgggagctgacgacgtgtcaa-B 3′(SEQ ID NO: 9315)The reaction was overlaid with mineral oil and preincubated for 10 minat 95° C. Amplification was performed for 15 cycles as follows: 94° C.for 15 sec, 65° C. for 1 min. A second 25 μl aliquot of the reactionmixture was added through the mineral oil containing 25 pmol each ofuniversal primers A and B. Cycling was repeated using 55° C. annealingtemperature. The reaction was next digested with a 2 μl solution of 1mg/ml Proteinase K/50 mM EDTA at 55° C. for 10 min. Proteinase K waseliminated by a final incubation at 90° C. for 15 min. For LDR,oligonucleotide synthesis and purification were carried out aspreviously described (Khanna et al., “Multiplex PCR/LDR for Detection ofK-ras Mutations in Primary Colon Tumors,” Oncogene 18:27-38 (1999),which is hereby incorporated by reference). Tth DNA ligase wasoverproduced and purified as described elsewhere (Luo et al.,“Identification of Essential Residues in Thermus thermophilus DNALigase,” Nucleic Acids Research 24: 3079-3085 (1996) and Barany et al.,“Cloning, Overexpression, and Nucleotide Sequence of a Thermostable DNALigase Gene,” Gene 109:1-11 (1991), which are hereby incorporated byreference). LDR was performed in a 20 μl reaction containing 500 fmol ofeach probe, 2 μl of amplified DNA and 20 mM Tris-HCl, pH 7.6; 10 mMMgCl₂; 100 mM KCl; 10 mM DTT; 1 mM NAD⁺. The reaction was heated to 94°C. for 1.5 min prior to adding 25 fmol of Tth DNA ligase and thensubjected to 20 cycles of 15 sec at 94° C. and 4 min at 65° C. (SeeTable 4).

Using the three BRCA1 and BRCA2 founder mutations in the AshkenaziJewish population (BRCA1 185delAG; BRCA1 5382insC; BRCA2 6174delT)(Rahman et al., “The Genetics of Breast Cancer Susceptibility,” Annu.Rev. Genet. 32:95-121 (1998), which is hereby incorporated by reference)as a model system, the assay readily detected these mutations inmultiplexed reactions in over 80 DNA samples. FIG. 21A shows arepresentative LDR gel detecting the three BRCA mutations. Byfluorescent end-labeling the discriminating upstream oligonucleotideswith either FAM (for wild-type) or TET (for mutant), and by addingdifferent length “tails” to LDR oligonucleotide probes, ligationproducts were easily distinguished based on label and migration on apolyacrylamide gel. Wild-type products are identified at the right sideof the gel. Mutant products are identified at the top of the gel.Electrophoretic separation was performed at 1400 volts using 8 Murea-10% polyacrylamide gels and an ABI 373 DNA sequencer. Fluorescentligation products were analyzed and quantified using the ABI Gene Scan672 software.

The analysis was next extended to detect the mutations in pooled samplesof DNA. DNAs with known mutations were diluted 1:2, 1:5, 1:10, and 1:20with wild-type DNA prior to PCR amplification and then subjected to LDR.These simulation experiments showed PCR/PCR/LDR could successfullydetect the presence of all three mutations when known mutant DNA wasdiluted 1:20 in wild-type DNA prior to amplification. FIG. 21B showsBRCA1 and BRCA2 mutation detection on pooled samples of DNA. DNA sampleswith known mutations were diluted into wild-type DNA prior toamplification. Ligation products from multiplex LDR are shown for eachdilution. BRCA1 del AG, BRCA1 ins C, and BRCA2 del T mean that only onemutation is present; multiplex LDR directed against only mutantsequences use 500 fmol of each LDR oligonucleotide probes. 3 mutationsmeans that all three mutations are present; multiplex LDR directedagainst mutant sequences only use 500 fmol of each LDR oligonucleotide.3 mutations+wild-type controls at 1:20 mean that all three mutations arepresent; multiplex LDR are directed against both mutant and wild-typesequences using 500 fmol and 25 fmol of each LDR oligonucleotide probes,respectively. The pooling experiment was repeated using 249 blindedAshkenazi Jewish DNA samples. Tubes containing the blinded DNAs wereassembled into a 9×9 gridded format and aliquots from each tube werecombined across the rows and then down the columns to produce one tubeof combined DNA for each row and each column. This was done to uniquelyclassify each sample using points of intersection on the gridded format.The pooled DNA was then subjected to amplification and LDR as describedabove. 248 of the 249 samples were correctly typed. The single samplethat was incorrectly identified as wild-type proved to be too dilute andfell below the limits of detection when mixed with 9 other samples ofhigher concentration. The number of individual reactions carried out wasreduced from 249 to 96 by this strategy (55 pooled samples and 41individual samples used for confirmation).

In addition to gel-based detection, mutation identification was alsoaccomplished by screening reaction products with a universal DNAmicroarray (Gerry et al., “Universal DNA Microarray Method for MultiplexDetection of Low Abundance Point Mutations,” J Mol Bio. 292:251-262(1999), which is hereby incorporated by reference). Microarrays wereprocessed and spotted as previously described (Gerry et al., “UniversalDNA Microarray Method for Multiplex Detection of Low Abundance PointMutations,” J Mol Bio. 292:251-262 (1999), which is hereby incorporatedby reference) using a Pixsys5500 robot enclosed in a humidity chamber(Cartesian Technologies, Irvine, Calif.). Briefly, LDR reactions werehybridized in 32 μl containing 300 mM MES, pH 6.0, 10 mM MgCl₂, 0.1% SDSat 65° C. for 1 h in a rotating chamber. After washing in 300 mM bicine,pH 8.0, 10 mM MgCl₂, 0.1% SDS for 10 min at 25° C. The array was imagedon an Olympus Provis AX70 microscope using a 100 W mercury burner, aTexas Red filter cube, and a Princeton Instruments TEK512/CCD camera.The 16-bit greyscale images were captured using MetaMorph Imaging System(Universal Imaging Corporation, West Chester, Pa.) and rescaled to morenarrowly bracket the LDR signal before conversion to 8-bit greyscale.The 8-bit images were colored using Adobe Photoshop to render the Cy3signal red.

Preliminary microarray experiments using probes designed in thegel-based format (i.e., differentially labeled discriminating probes andidentical common probes) demonstrated that wild-type and mutant versionsof the three BRCA sequences were readily detected on the array (see WO97/31256 to Barany et al., which is hereby incorporated by reference).In this version, both types of sequences were directed to the sameaddresses (e.g., BRCA1 185delAG and BRCA1 185 wild-type were bothdirected to zip-code 1). Although this format proved successful,PCR/PCR/LDR has the potential of detecting hundreds of mutations in asingle-tube reaction and this design does not make optimal use of thearray for such large-scale mutation detection experiments. In order toestablish the experimental paradigm for future studies, the addressableformat was expanded by choosing a sequence in each of the amplicons touse as a control an LDR ligation product. Thus, rather than requiredetection of wild-type sequences for each mutant LDR product, thisformat uses a single product to serve as a positive control for multipledifferent sequence variants within an amplicon (see FIG. 22). Oneadvantage of this format is that it minimizes oligonucleotide synthesis;additionally, the use of each of the 64 positions is maximized. Sincethe number of LDR ligation products that can be detected at a singleaddress is limited by the number of currently available spectrallyseparated fluorescent labels, confining the control to a specifiedregion of the array permits one more sequence variant to be detected ateach remaining address. In the experiments described below, control andmutant LDR ligation products for a queried position were directed to sixseparate addresses on a 64 position array.

All three frameshift mutations were detectable by hybridization to theuniversal array (FIG. 23). FIG. 23A shows the assignment of each controland mutant sequence to specific addresses on the array surface. Controlsignals are directed to the upper three addresses; mutant signals areassigned to the lower three. FIG. 23B shows signal produced by awild-type DNA. FIGS. 23C, E, and G show representative hybridizationsfor individual DNA samples. FIGS. 23D, F, and H show representativehybridizations for each mutation using pooled samples of DNA fromAshkenazi individuals. The mutations are identified on the extremeright.

Only combinations of the six possible addresses were visible followinghybridization and no additional signals were detected at any of theunused addresses. Thus, zip-code hybridization is very specific. Controland mutant signals were clearly present for each of the mutationsderived from samples of DNA from single individuals (FIGS. 23C, E, andG). Pooled DNA used in analyzing the 249 DNA samples described aboveproduced signals for mutations identical to those found in the gel-basedassay (FIGS. 23D, F, and H). In each case, the array reproduced theresult of the gel.

These results demonstrate that universal microarray analysis ofPCR/PCR/LDR products permits rapid identification of small insertion anddeletion mutations in the context of both clinical diagnosis andpopulation studies.

Example 3—p53 Chip Hybridization and Washing Conditions

Three parameters (presence or absence of non-specific DNA competitor,temperature, and wash buffer composition) were varied in differentcombinations in order to determine which method would produce minimumbackground noise without significant loss of signal. Hybridization wasperformed with 100 μg/ml of sheared salmon sperm DNA (FIGS. 16B, D, J,and L), 250 μg/ml of sheared salmon sperm DNA (FIGS. 16F, H, N, and P),or no non-specific competitor DNA (FIGS. 16A, C, E, G, I, K, M, and O).Washing was performed for 10 min using four different conditions: roomtemperature in standard wash buffer (300 mM bicine, pH 8.0, 10 mM MgCl₂,0.1% SDS) (FIGS. 16A, B, E, and F); room temperature in standard washbuffer supplemented with 10% formamide (FIGS. 161, J, M, and N); 50° C.in standard wash buffer (FIGS. 16C, D, G, and H); or 50° C. in standardwash buffer supplemented with 10% formamide (FIGS. 16K, L, O, and P).The numbers on the upper right of each panel indicate the density ofpixels for p53 exon 5 control (zip-code 1) for each condition. Thepercent of loss indicated on the right side of the figure compares theleft and right panel directly adjacent to calculated percentage.Fiducials (Cy3, Cy5, and fluorescein) are spotted horizontally on theupper left and vertically on the lower right regions of the chips togive orientation. Zip-code 1 is located directly below the fiducial inthe upper left area; subsequent zip-codes are spotted in numerical orderin a left to right manner.

PCR was carried out as a single-tube, multiplex reaction in order tosimultaneously amplify p53 exons 5 and 7. Commercially available genomicDNA from lymphocytes was amplified in a 25 μl reaction mixturecontaining 100 ng of DNA, 400 μM of each dNTP, 1×PCR Buffer II (10 mMTris-HCl pH 8.3 at 25° C., 50 mM KCl) supplemented with 4 mM MgCl₂, 1 UAmpliTaq Gold and 2 pmol of each gene-specific primer bearing eitheruniversal primer A or B on the 5′ ends (see Table 5). The reaction wasoverlaid with mineral oil and preincubated for 10 min at 95° C.Amplification was performed for 15 cycles as follows: 94° C. for 15 sec,65° C. for 1 min. A second 25 μl aliquot of the reaction mixture wasadded through the mineral oil containing 25 pmol each of universalprimers A and B. Cycling was repeated using 55° C. annealingtemperature. The reaction was next digested with a 2 μl solution of 1mg/ml Proteinase K/50 mM EDTA at 55° C. for 10 min. Proteinase K waseliminated by a final incubation at 90° C. for 15 min. For LDR,oligonucleotide synthesis and purification were carried out aspreviously described (Khanna et al., “Multiplex PCR/LDR for Detection ofK-ras Mutations in Primary Colon Tumors,” Oncogene 18:27-38 (1999),which is hereby incorporated by reference). Tth DNA ligase wasoverproduced and purified as described elsewhere (Luo et al.,“Identification of Essential Residues in Thermus thermophilus DNALigase,” Nucleic Acids Research 24:3079-3085 (1996) and Barany et al.,“Cloning, Overexpression, and Nucleotide Sequence of a Thermostable DNALigase Gene,” Gene 109:1-11 (1991), which are hereby incorporated byreference). LDR was performed in a 20 μl reaction containing 500 fmol ofeach probe, 2 μl of amplified DNA and 20 mM Tris-HCl, pH 7.6; 10 mMMgCl₂; 100 mM KCl; 10 mM DTT; 1 mM NAD⁺. The reactants were heated to94° C. for 1.5 min prior to adding 25 fmol of Tth DNA ligase and thensubjected to 20 cycles of 15 sec at 94° C. and 4 min at 65° C. See Table5 which shows the oligonucleotide primers and probes designed to detectmutations in p53 by PCR/LDR/array hybridization as follows:

TABLE 5 Primers and Probes Designed for Mutation Detection in p53 byPCR/LDR/Array Hybridization. Primer/Probe Sequence (5′→3′) Uni A primerGGAGCACGCTATCCCGTTAGAC (SEQ ID NO: 9316) Uni B2 primerCGCTGCCAACTACCGCACATC (SEQ ID NO: 9317) p53X5FzipAGGAGCACGCTATCCCGTTAGACCTGTTCACTTGTGCCCTGACTTTC (SEQ ID NO: 9318)p53X5RzipB CGCTGCCAACTACCGCACATCCCAGCTGCTCACCATCGCTATC (SEQ ID NO: 9319)K132LA2G Fam-aaaGCCAGTTGGCAAAACATCC (SEQ ID NO: 9320) K132LA2G3Cy3-GCCAGTTGGCAAAACATCC (SEQ ID NO: 9321) K132LA2GCOMpTGTTGAGGGCAGGGGAGTACTGTAaaa-B (SEQ ID NO: 9322) K132LA2Gzip9pTGTTGAGGGCAGGGGAGTACTGTA-catcgtccctttcgatgggatcaa-B (SEQ ID NO: 9323)C135UGA Fam-CTGCCCTCAACAAGATGTTTTA (SEQ ID NO: 9324) C135UGA3Cy3-CTGCCCTCAACAAGATGTTTTA (SEQ ID NO: 9325) C135UGCompCCAACTGGCCAAGACCTGCCaaaa-B (SEQ ID NO: 9326) C135UGTFam-CTGCCCTCAACAAGATGTTTTT (SEQ ID NO: 9327) C135UGT5Cy5-CTGCCCTCAACAAGATGTTTTT (SEQ ID NO: 9328) C135UGzip10pCCAACTGGCCAAGACCTGCC-caaggcacgtcccagacgcatcaa-B (SEQ ID NO: 9329)C141UGA Tet-GCCAACTGGCCAAGACCTA (SEQ ID NO: 9330) C141UGA3Cy3-GCCAACTGGCCAAGACCTA (SEQ ID NO: 9331) C141UGCompCCCTGTGCAGCTGTGGGTTGAaaaaa-B (SEQ ID NO: 9332) C141UGzip11pCCCTGTGCAGCTGTGGGTTGA-gcacgggagctgacgacgtgtcaa-B (SEQ ID NO: 9333)V143UGA Fam-TGGCCAAGACCTGCCCTA (SEQ ID NO: 9334) V143UGA3Cy3-TGGCCAAGACCTGCCCTA (SEQ ID NO: 9335) V143UGACOMpTGCAGCTGTGGGTTGATTCCAaaa-B (SEQ ID NO: 9336) V143UGAzip12pTGCAGCTGTGGGTTGATTCCA-agacgcaccgcaacaggctgtcaa-B (SEQ ID NO: 9337)V143UTC Fam-CCAAGACCTGCCCTGC (SEQ ID NO: 9338) V143UTC3Cy3-CCAAGACCTGCCCTGC (SEQ ID NO: 9339) V143UTCOMpGCAGCTGTGGGTTGATTCCACAaaaa-B (SEQ ID NO: 9340) V143UTzip13pGCAGCTGTGGGTTGATTCCACA-catcgctgcaagtaccgcactcaa-B (SEQ ID NO: 9341)W146UG3A3 Cy3-TGCCCTGTGCAGCTGTGA (SEQ ID NO: 9342) W146UG3zippGTTGATTCCACACCCCCGCC-cgatggcttccttacccagattcg-B (SEQ ID NO: 9343)P152LC2T2 Tet-CGGGTGCCGGGCA (SEQ ID NO: 9344) P152LC2T23Cy3-CGGGTGCCGGGCA (SEQ ID NO: 9344) P152LC2T2COMpGGGGTGTGGAATCAACCCACAaaaaaa-B (SEQ ID NO: 9345) P152Lzip14pGGGGTGTGGAATCAACCCACA-ggctgggacgtgcagaccgttcaa-B (SEQ ID NO: 9346)G154LG1A Fam-atataaCACACCCCCGCCCA (SEQ ID NO: 9347) G154LG1A3Cy3-CACACCCCCGCCCA (SEQ ID NO: 9348) G154LG1ACompGCACCCGCGTCCGCGatataa-B (SEQ ID NO: 9349) G154LG1Azip15pGCACCCGCGTCCGCG-gctggctggcacgcaccagaatca-B (SEQ ID NO: 9350) V157LGCTet-GCCATGGCGCGGAG (SEQ ID NO: 9351) V157LGC5Cy5-GCCATGGCGCGGAG (SEQ ID NO: 9351) V157LGCOMpGCGGGTGCCGGGCGaaa-B (SEQ ID NO: 9352) V157LGTTet-GCCATGGCGCGGAA (SEQ ID NO: 9353) V157LGT3Cy3-GCCATGGCGCGGAA (SEQ ID NO: 9353) V157LGzip16pGCGGGTGCCGGGCG-ggctccgtcagaaagcgacaatca-B (SEQ ID NO: 9354) R158LC1A5Cy5-GATGGCCATGGCGCT (SEQ ID NO: 9355) R158LC1zippGACGCGGGTGCCGGG-acgagggatacccgcaaacgatca-B (SEQ ID NO: 9356) R158UGATet-CGGCACCCGCGTCCA (SEQ ID NO: 9357) R158UGA3Cy3-CGGCACCCGCGTCCA (SEQ ID NO: 9357) R158UGACOMpCGCCATGGCCATCTACAAGC-B (SEQ ID NO: 9358) R158UGAzip17pCGCCATGGCCATCTACAAGC-acgagggatacccgcaaacgatca-B (SEQ ID NO: 9359)A161LC2T5 Cy5-GTGCTGTGACTGCTTGTAGATGA (SEQ ID NO: 9360) A161LC2TzippCCATGGCGCGGACGC-gggaggctgctgtcctttcgatca-B (SEQ ID NO: 9361) A161UGATet-aaaaaaaaGCGTCCGCGCCATGA (SEQ ID NO: 9362) A161UGA3Cy3-GCGTCCGCGCCATGA (SEQ ID NO: 9363) A161UGCOMpCCATCTACAAGCAGTCACAGCACAaaaaaaaa-B (SEQ ID NO: 9364) A161UGzip18pCCATCTACAAGCAGTCACAGCACA-gggaggctgctgtcctttcgatca-B (SEQ ID NO: 9365)V173UGA Fam-CACAGCACATGACGGAGGTTA (SEQ ID NO: 9366) V173UGA3Cy3-CACAGCACATGACGGAGGTTA (SEQ ID NO: 9366) V173UGCOMpTGAGGCGCTGCCCCCAaaaaa-B (SEQ ID NO: 9367) V173UGTFam-CACAGCACATGACGGAGGTTT (SEQ ID NO: 9368) V173UGT5Cy5-CACAGCACATGACGGAGGTTT (SEQ ID NO: 9368) V173UGzip19pTGAGGCGCTGCCCCCA-acagcgtgttcgttgcttgcatca-B (SEQ ID NO: 9369)R175LC1Com pCCTCACAACCTCCGTCATGTGCT-B (SEQ ID NO: 9370) R175LC1TFam-CATGGTGGGGGCAGCA (SEQ ID NO: 9371) R175LC1T3Cy3-CATGGTGGGGGCAGCA (SEQ ID NO: 9371) R175LC1zip20pCCTCACAACCTCCGTCATGTGCT-atggcgatggtccactcgcaatca-B (SEQ ID NO: 9372)R175LG2T Fam-CTCATGGTGGGGGCAGT (SEQ ID NO: 9373) R175LG2T5Cy5-CTCATGGTGGGGGCAGT (SEQ ID NO: 9373) R175LG2TCOMpGCCTCACAACCTCCGTCATGTG-B (SEQ ID NO: 9374) R175LG2Tzip21pGCCTCACAACCTCCGTCATGTG-gtccgtccatggcaagcgtgatca-B (SEQ ID NO: 9375)R175UG2A Tet-TGACGGAGGTTGTGAGGCA (SEQ ID NO: 9376) R175UG2A3Cy3-TGACGGAGGTTGTGAGGCA (SEQ ID NO: 9376) R175UG2ACompCTGCCCCCACCATGAGCGaaaaaa-B (SEQ ID NO: 9377) R175UG2Azip21pCTGCCCCCACCATGAGCG-gtccgtccatggcaagcgtgatca-B (SEQ ID NO: 9378) C176UGAFam-CGGAGGTTGTGAGGCGCTA (SEQ ID NO: 9379) C176UGA5Cy5-CGGAGGTTGTGAGGCGCTA (SEQ ID NO: 9379) C176UGCompCCCCCACCATGAGCGCTGaaaaaaa-B (SEQ ID NO: 9380) C176UGTFam-CGGAGGTTGTGAGGCGCTT (SEQ ID NO: 9381) C176UGT3Cy3-CGGAGGTTGTGAGGCGCTT (SEQ ID NO: 9381) C176UGzip22pCCCCCACCATGAGCGCTG-ggctgcacccgttgaggcacatca-B (SEQ ID NO: 9382)H179LACOM pGGTGGGGGCAGCGCC-B (SEQ ID NO: 9383) H179LAGFam-GCTATCTGAGCAGCGCTCAC (SEQ ID NO: 9384) H179LAG3Cy3-GCTATCTGAGCAGCGCTCAC (SEQ ID NO: 9384) H179LATFam-GCTATCTGAGCAGCGCTCAA (SEQ ID NO: 9385) H179LAT5Cy5-GCTATCTGAGCAGCGCTCAA (SEQ ID NO: 9385) H179LAzip23pGGTGGGGGCAGCGCC-tcaacatcggctaacggtccatca-B (SEQ ID NO: 9386) H179LCTFam-GCTATCTGAGCAGCGCTCATA (SEQ ID NO: 9387) H179LCT3Cy3-GCTATCTGAGCAGCGCTCATA (SEQ ID NO: 9387) H179LCTCOMpGTGGGGGCAGCGCCTCAC-B (SEQ ID NO: 9388) H179LCTzip24pGTGGGGGCAGCGCCTCAC-cgcacgcagtcctcctccgtatca-B (SEQ ID NO: 9389) X5LCompCGGGGGTGTGGAATCAACCC-B (SEQ ID NO: 9390) X5LWTFam-CGCGGGTGCCGGG (SEQ ID NO: 9391) X5LWT3Cy3-CGCGGGTGCCGGG (SEQ ID NO: 9391) X5LWT5Cy5-CGCGGGTGCCGGG (SEQ ID NO: 9391) X5Lzip1pCGGGGGTGTGGAATCAACCC-cgcagattttgcgctggatttcaa-B (SEQ ID NO: 9392)p53X6FzipA GGAGCACGCTATCCCGTTAGACCCTCTGATTCCTCACTGATTGCTCTTA(SEQ ID NO: 9393) p53X6RzipBCGCTGCCAACTACCGCACATCGGCCACTGACAACCACCCTTAAC (SEQ ID NO: 9394) P190LCTTet-aaaaTCGGATAAGATGCTGAGGAGA (SEQ ID NO: 9395) P190LCT3Cy3-TCGGATAAGATGCTGAGGAGA (SEQ ID NO: 9396) P190LCTCOMpGGCCAGACCCTAAGAGCAATCAGaaaa-B (SEQ ID NO: 9397) P190LCTzip25pGGCCAGACCCTAAGAGCAATCAG-ggctcgcaggctggctcatcctaa-B (SEQ ID NO: 9398)P190LTA5 Cy5-CACTCGGATAAGATGCTGAGGT (SEQ ID NO: 9399) P190LTAzippGGGGCCAGACCCTAAGAGCAA-ggctcgcaggctggctcatcctaa-B (SEQ ID NO: 9400)H193LAG3 Cy3-AATTTCCTTCCACTCGGATAAGAC (SEQ ID NO: 9401) H193LAGzippGCTGAGGAGGGGCCAGACC-cgcattcgatggacaggacattcg-B (SEQ ID NO: 9402)H193LTA5 Cy5-AATTTCCTTCCACTCGGATAAGT (SEQ ID NO: 9403) H193LTAzippTGCTGAGGAGGGGCCAGAC-cgcattcgatggacaggacattcg-B (SEQ ID NO: 9404)R196LCCom pGATAAGATGCTGAGGAGGGGCCA-B (SEQ ID NO: 9405) R196LCTFam-CGCAAATTTCCTTCCACTCA (SEQ ID NO: 9406) R196LCT3Cy3-CGCAAATTTCCTTCCACTCA (SEQ ID NO: 9406) R196LCzip26pGATAAGATGCTGAGGAGGGGCCA-cgcatgaggggaaacgacgagatt-B (SEQ ID NO: 9407)Y205LAC Fam-AAAAGTGTTTCTGTCATCCAAAG (SEQ ID NO: 9408) Y205LAC3Cy3-AAAAGTGTTTCTGTCATCCAAAG (SEQ ID NO: 9408) Y205LACOMpACTCCACACGCAAATTTCCTTCCAaaaaaa-B (SEQ ID NO: 9409) Y205LAGFam-AAAAGTGTTTCTGTCATCCAAAC (SEQ ID NO: 9410) Y205LAG5Cy5-AAAAGTGTTTCTGTCATCCAAAC (SEQ ID NO: 9410) Y205LAzip27pACTCCACACGCAAATTTCCTTCCA-gcaccgtgaacgacagttgcgatt-B (SEQ ID NO: 9411)T211LAG Tet-CCACCACACTATGTCGAAAAGC (SEQ ID NO: 9412) T211LAG3Cy3-CCACCACACTATGTCGAAAAGC (SEQ ID NO: 9412) T211LAGCOMpGTTTCTGTCATCCAAATACTCCACACGaaa-B (SEQ ID NO: 9413) T211LAGzip28pGTTTCTGTCATCCAAATACTCCACACG-cgcaggtcgctgcgtgtcctgatt-B(SEQ ID NO: 9414) T211LCT Tet-ACCACCACACTATGTCGAAAAA (SEQ ID NO: 9415)T211LCT3 Cy3-ACCACCACACTATGTCGAAAAA (SEQ ID NO: 9415) T211LCTCOMpTGTTTCTGTCATCCAAATACTCCACACaaa-B (SEQ ID NO: 9416) T211LCTzip29pTGTTTCTGTCATCCAAATACTCCACAC-cgcaaagcagacacagggtcgatt-B(SEQ ID NO: 9417) R213LCCompAAAAGTGTTTCTGTCATCCAAATACTCCa-B (SEQ ID NO: 9418) R213LCTTet-GGGCACCACCACACTATGTCA (SEQ ID NO: 9419) R213LCT3Cy3-GGGCACCACCACACTATGTCA (SEQ ID NO: 9419) R213LCzip30pAAAAGTGTTTCTGTCATCCAAATACTCC-catcgcacttcgctttggctgatt-B(SEQ ID NO: 9420) Y220LACom pAGGGCACCACCACACTATGTCGA-B (SEQ ID NO: 9421)Y220LAG Tet-CAGACCTCAGGCGGCTCAC (SEQ ID NO: 9422) Y220LAG3Cy3-CAGACCTCAGGCGGCTCAC (SEQ ID NO: 9422) Y220LAzip31pAGGGCACCACCACACTATGTCGA-ttgcgggaactcacgaggtcgtat-B (SEQ ID NO: 9423)X6UCOM pCCTATGAGCCGCCTGAGGTCTaaaa-B (SEQ ID NO: 9424) X6UWTFam-aaaTTCGACATAGTGTGGTGGTGC (SEQ ID NO: 9425) X6UWT3Cy3-TTCGACATAGTGTGGTGGTGC (SEQ ID NO: 9545) X6UWT5Cy5-TTCGACATAGTGTGGTGGTGC (SEQ ID NO: 9545) X6Uzip2pCCTATGAGCCGCCTGAGGTCT-ttcgccgtcgtgtaggcttttcaa-B (SEQ ID NO: 9426)p53X7FzipA GGAGCACGCTATCCCGTTAGACGCCTCATCTTGGGCCTGTGTTATC(SEQ ID NO: 9427) p53X7RzipBCGCTGCCAACTACCGCACATCGTGGATGGGTAGTAGTATGGAAGAAATC (SEQ ID NO: 9428)Y234UTA3 Cy3-CTCTGACTGTACCACCATCCACA (SEQ ID NO: 9429) Y234UTAzippACAACTACATGTGTAACAGTTCCTGCAT-ggctacgacgcatgtaaacgttcg-B(SEQ ID NO: 9430) M237UGAFam-aaaaATAAGTACCACCATCCACTACAACTACATA (SEQ ID NO: 9431) M237UGA3Cy3-ATAAGTACCACCATCCACTACAACTACATA (SEQ ID NO: 9432) M237UGCOMpTGTAACAGTTCCTGCATGGGCGaaaa-B (SEQ ID NO: 9433) M237UGTFam-aaaaATAAGTACCACCATCCACTACAACTACATT (SEQ ID NO: 9434) M237UGT5Cy5-ATAAGTACCACCATCCACTACAACTACATT (SEQ ID NO: 9435) M237UGzip32pTGTAACAGTTCCTGCATGGGCG-gcacggctcgataggtcaagcttt-B (SEQ ID NO: 9436)C238UGA Tet-CCACCATCCACTACAACTACATGTA (SEQ ID NO: 9437) C238UGA3Cy3-CCACCATCCACTACAACTACATGTA (SEQ ID NO: 9437) C238UGCompTAACAGTTCCTGCATGGGCGGaaaaa-B (SEQ ID NO: 9438) C238UGzip33pTAACAGTTCCTGCATGGGCGG-cgatttcgactcaagcggctcttt-B (SEQ ID NO: 9439)S241LC2A6 Fam-ATGCCGCCCATGCAGT (SEQ ID NO: 9440) S241LC2AzippAACTGTTACACATGTAGTTGTAGTGGATGGT-cgcaatggtaggtgagcaagcaga-B(SEQ ID NO: 9441) S241LCCompAACTGTTACACATGTAGTTGTAGTGGATGGTaaa-B (SEQ ID NO: 9442) S241LCGFam-TGCCGCCCATGCAGC (SEQ ID NO: 9443) S241LCG5Cy5-TGCCGCCCATGCAGC (SEQ ID NO: 9443) S241LCTFam-TGCCGCCCATGCAGA (SEQ ID NO: 9444) S241LCT3Cy3-TGCCGCCCATGCAGA (SEQ ID NO: 9444) S241LCzip34pAACTGTTACACATGTAGTTGTAGTGGATGGT-cgcaatggtaggtgagcaagcaga-B(SEQ ID NO: 9445) G244UG1TFam-aaaaaCATGTGTAACAGTTCCTGCATGT (SEQ ID NO: 9446) G244UG1T3Cy3-CATGTGTAACAGTTCCTGCATGT (SEQ ID NO: 9447) G244UG1TCOMpGCGGCATGAACCGGAGGCaaaaaa-B (SEQ ID NO: 9448) G244UG1Tzip35pGCGGCATGAACCGGAGGC-gtccccgttacctaggcgatcaga-B (SEQ ID NO: 9449)G244UG2A Fam-aaaaaaTGTGTAACAGTTCCTGCATGGA (SEQ ID NO: 9450) G244UG2A3Cy3-TGTGTAACAGTTCCTGCATGGA (SEQ ID NO: 9451) G244UG2COMpCGGCATGAACCGGAGGCCaaaaaa-B (SEQ ID NO: 9452) G244UG2TFam-aaaaaaTGTGTAACAGTTCCTGCATGGT (SEQ ID NO: 9453) G244UG2T5Cy5-TGTGTAACAGTTCCTGCATGGT (SEQ ID NO: 9454) G244UG2zip36pCGGCATGAACCGGAGGCC-atgggtccacagtaccgctgcaga-B (SEQ ID NO: 9455)G245UG1A Tet-AACAGTTCCTGCATGGGCA (SEQ ID NO: 9456) G245UG1A3Cy3-AACAGTTCCTGCATGGGCA (SEQ ID NO: 9456) G245UG1ACompGCATGAACCGGAGGCCCAaaaa-B (SEQ ID NO: 9457) G245UG1Azip37pGCATGAACCGGAGGCCCA-ccgtgggagattaggtggctcaga-B (SEQ ID NO: 9458)G245UG2A Fam-CAGTTCCTGCATGGGCGA (SEQ ID NO: 9459) G245UG2A3Cy3-CAGTTCCTGCATGGGCGA (SEQ ID NO: 9459) G245UG2ACompCATGAACCGGAGGCCCATCaaa-B (SEQ ID NO: 9460) G245UG2Azip38pCATGAACCGGAGGCCCATC-gggaatggaggtgggaacgagaca-B (SEQ ID NO: 9461)G245UG2T Tet-aaaaaaaaAGTTCCTGCATGGGCGA (SEQ ID NO: 9462) G245UG2T5Cy5-CAGTTCCTGCATGGGCGT (SEQ ID NO: 9463) G245UG2TCOMpCATGAACCGGAGGCCCATCaaaaaaaaa-B (SEQ ID NO: 9464) R248LCCompGTTCATGCCGCCCATGCAaa-B (SEQ ID NO: 9465) R248LCTTet-GGTGAGGATGGGCCTCCA (SEQ ID NO: 9466) R248LCT3Cy3-GGTGAGGATGGGCCTCCA (SEQ ID NO: 9466) R248LCzip39pGTTCATGCCGCCCATGCA-cgtggctgactcgctgcgatgaca-B (SEQ ID NO: 9467) R248UGATet-TGGGCGGCATGAACCA (SEQ ID NO: 9468) R248UGA3Cy3-TGGGCGGCATGAACCA (SEQ ID NO: 9468) R248UGCompGAGGCCCATCCTCACCATCATaa-B (SEQ ID NO: 9469) R248UGzip40pGAGGCCCATCCTCACCATCAT-ttgcgcaccatcaggttagggaca-B (SEQ ID NO: 9470)R249LACom pCCGGTTCATGCCGCCCAa-B (SEQ ID NO: 9471) R249LAGFam-TGATGGTGAGGATGGGCCC (SEQ ID NO: 9472) R249LAG5Cy5-TGATGGTGAGGATGGGCCC (SEQ ID NO: 9472) R249LATFam-TGATGGTGAGGATGGGCCA (SEQ ID NO: 9473) R249LAT3Cy3-TGATGGTGAGGATGGGCCA (SEQ ID NO: 9473) R249LAzip41pCCGGTTCATGCCGCCCA-gcaccgatatggagaccgcagaca-B (SEQ ID NO: 9474) R249LG3CTet-GATGATGGTGAGGATGGGG (SEQ ID NO: 9475) R249LG3C3Cy3-GATGATGGTGAGGATGGGG (SEQ ID NO: 9475) R249LG3CompCTCCGGTTCATGCCGCC-B (SEQ ID NO: 9476) R249LG3zip42pCTCCGGTTCATGCCGCC-catcgacaaggtaacgcgtggaca-B (SEQ ID NO: 9477)P250LC2T3 Cy3-AGTGTGATGATGGTGAGGATGA (SEQ ID NO: 9478) P250LC2TzippGCCTCCGGTTCATGCCG-gtcccaagttgcggctcactttcg-B (SEQ ID NO: 9479) I254LAGFam-CTGGAGTCTTCCAGTGTGATGAC (SEQ ID NO: 9480) I254LAG3Cy3-CTGGAGTCTTCCAGTGTGATGAC (SEQ ID NO: 9480) I254LAGCOMpGGTGAGGATGGGCCTCCG-B (SEQ ID NO: 9481) I254LAGzip43pGGTGAGGATGGGCCTCCG-tgagcgcaaggtcagagcacgaca-B (SEQ ID NO: 9482) X7LCompCATGCAGGAACTGTTACACATGTAGTTGTAa-B (SEQ ID NO: 9483) X7LWTTet-TCCGGTTCATGCCGCC (SEQ ID NO: 9484) X7LWT3Cy3-TCCGGTTCATGCCGCC (SEQ ID NO: 9484) X7LWT5Cy5-TCCGGTTCATGCCGCC (SEQ ID NO: 9484) X7Lzip3pCATGCAGGAACTGTTACACATGTAGTTGTA-ccgtaagcccgtatggcagatcaa-B(SEQ ID NO: 9485) p53X8FzipAGGAGCACGCTATCCCGTTAGACGGACAGGTAGGACCTGATTTCCTTAC (SEQ ID NO: 9486)p53X8RzipB CGCTGCCAACTACCGCACATCCGCTTCTTGTCCTGCTTGCTTAC(SEQ ID NO: 9487) F270UTATet-aaaaaATCTACTGGGACGGAACAGCA (SEQ ID NO: 9488) F270UTA3Cy3-ATCTACTGGGACGGAACAGCA (SEQ ID NO: 9489) F270UTCOMpTTGAGGTGCGTGTTTGTGCCTaaaaaa-B (SEQ ID NO: 9490) F270UTzip44pTTGAGGTGCGTGTTTGTGCCT-aagccgcagcacgattccgtgaca-B (SEQ ID NO: 9491)V272UGA Fam-aaaaaaGGACGGAACAGCTTTGAGA (SEQ ID NO: 9492) V272UGA3Cy3-GGACGGAACAGCTTTGAGA (SEQ ID NO: 9493) V272UGCOMpTGCGTGTTTGTGCCTGTCCTGGaaaaaaa-B (SEQ ID NO: 9494) V272UGTFam-aaaaaaGGACGGAACAGCTTTGAGT (SEQ ID NO: 9495) V272UGT5Cy5-GGACGGAACAGCTTTGAGT (SEQ ID NO: 9496) V272UGzip45pTGCGTGTTTGTGCCTGTCCTGG-tgagaagcgtccaagccagaacga-B (SEQ ID NO: 9497)R273LCCom pCACCTCAAAGCTGTTCCGTCCCaa-B (SEQ ID NO: 9498) R273LCTTet-CCAGGACAGGCACAAACACA (SEQ ID NO: 9499) R273LCT3Cy3-CCAGGACAGGCACAAACACA (SEQ ID NO: 9499) R273LCzip46pCACCTCAAAGCTGTTCCGTCCC-catccaaggtccgacacgcaacga-B (SEQ ID NO: 9500)R273UCA5 Cy5-ACGGAACAGCTTTGAGGTGA (SEQ ID NO: 9501) R273UCAzippGTGTTTGTGCCTGTCCTGGGAGA-catccaaggtccgacacgcaacga-B (SEQ ID NO: 9502)R273UGA Tet-CGGAACAGCTTTGAGGTGCA (SEQ ID NO: 9503) R273UGA3Cy3-CGGAACAGCTTTGAGGTGCA (SEQ ID NO: 9503) R273UGCompTGTTTGTGCCTGTCCTGGGAGaaaaaa-B (SEQ ID NO: 9504) R273UGzip47pTGTTTGTGCCTGTCCTGGGAG-ttcgacgattcgcatcaacgcaag-B (SEQ ID NO: 9505)C275UGA Tet-aaaaaaaAGCTTTGAGGTGCGTGTTTA (SEQ ID NO: 9506) C275UGA3Cy3-CAGCTTTGAGGTGCGTGTTTA (SEQ ID NO: 9507) C275UGCOMpTGCCTGTCCTGGGAGAGACCaaaaaaa-B (SEQ ID NO: 9508) C275UGTTet-aaaaaaaaCAGCTTTGAGGTGCGTGTTTT (SEQ ID NO: 9509) C275UGT5Cy5-CAGCTTTGAGGTGCGTGTTTT (SEQ ID NO: 9510) C275UGzip48pTGCCTGTCCTGGGAGAGACC-aacggggaaggttgagcgtgacag-B (SEQ ID NO: 9511)R280UGA Tet-TTTGTGCCTGTCCTGGGAA (SEQ ID NO: 9512) R280UGA3Cy3-TTTGTGCCTGTCCTGGGAA (SEQ ID NO: 9512) R280UGCOMpAGACCGGCGCACAGAGGAAGaaaaaa-B (SEQ ID NO: 9513) R280UGTTet-TTTGTGCCTGTCCTGGGAT (SEQ ID NO: 9514) R280UGT5Cy5-TTTGTGCCTGTCCTGGGAT (SEQ ID NO: 9514) R280UGzip49pAGACCGGCGCACAGAGGAAG-cactgcacacgaaacggcacacag-B (SEQ ID NO: 9515)D281UCA3 Cy3-GTGCCTGTCCTGGGAGAGAA (SEQ ID NO: 9516) D281UCAGzippCGGCGCACAGAGGAAGAGAA-aagcaagccaaggtatggattgc-B (SEQ ID NO: 9517)D281UCG5 Cy5-GTGCCTGTCCTGGGAGAGAG (SEQ ID NO: 9518) D281UGA3Cy3-TTGTGCCTGTCCTGGGAGAA (SEQ ID NO: 9519) D281UGACzippACCGGCGCACAGAGGAAGAG-cgtgcgcacactcactgtccttcg-B (SEQ ID NO: 9520)D281UGC5 Cy5-TTGTGCCTGTCCTGGGAGAC (SEQ ID NO: 9521) R282LCCompGTCTCTCCCAGGACAGGCACAAAaaa-B (SEQ ID NO: 9522) R282LCTFam-TCTCTTCCTCTGTGCGCCA (SEQ ID NO: 9523) R282LCT3Cy3-TCTCTTCCTCTGTGCGCCA (SEQ ID NO: 9523) R282LCzip50pGTCTCTCCCAGGACAGGCACAAA-taccgacatcctgggattgcatgg-B (SEQ ID NO: 9524)R282UG2A5 Cy5-CCTGTCCTGGGAGAGACCA (SEQ ID NO: 9525) R282UG2AzippGCGCACAGAGGAAGAGAATCTCC-taccgacatcctgggattgcatgg-B (SEQ ID NO: 9526)E286UGA3 Cy3-AGACCGGCGCACAGAGA (SEQ ID NO: 9527) E286UGAzippAAGAGAATCTCCGCAAGAAAGGG-ttcggctgacgtaggcaagaggt-B (SEQ ID NO: 9528)R306LCT Cy3-TTGTCCTGCTTGCTTACCTCA (SEQ ID NO: 9529) R306LCTFam-aaaaTTGTCCTGCTTGCTTACCTCA (SEQ ID NO: 9530) R306LCTCOMpCTTAGTGCTCCCTGGGGGCAGaaaaa-B (SEQ ID NO: 9531) R306LCTzip51pCTTAGTGCTCCCTGGGGGCAG-actccgcattgccagagctgatgg-B (SEQ ID NO: 9532)X8UCOM pCTCACCACGAGCTGCCCCC-B (SEQ ID NO: 9533) X8UWTFam-TCCGCAAGAAAGGGGAGC (SEQ ID NO: 9534) X8UWT3Cy3-TCCGCAAGAAAGGGGAGC (SEQ ID NO: 9534) X8UWT5Cy5-TCCGCAAGAAAGGGGAGC (SEQ ID NO: 9534) X8Uzip4pCTCACCACGAGCTGCCCCC-atggccgtgctggggacaagtcaa-B (SEQ ID NO: 9535) ThePCR primers are specifically designed to amplify regions within andsurrounding the p53 gene. After 15 rounds of amplification at high Tm's(i.e. 65° C.) using the longer gene-specific primers (at 1-2 pmoles perreaction), the two universal primers (bold upper case) are added at 50pmoles in 50 μl and products cycled for an additional 20 rounds ofamplification. The allele-specific LDR probes contained fluorescentlabels on the 5′-ends (Fam, Tet, Cy3 or Cy5) and the discriminatingbases on their 3′-ends. Non-genomic sequence was added to the 5′-ends ofsome probes (designated by bold lower case) to control the finalligation product size for gel-based assays. The common LDR probescontained 5′-phosphates (p) and C-3 blocking (B) groups on their3′-ends. Common LDR probes used in array-based detection have zipcodesequences (designated by lower case) on their 3′-ends.

LDR reactions were hybridized in 32 μl containing 300 mM MES, pH 6.0, 10mM MgCl₂ 0.1% SDS with or without 100 μg/ml sheared salmon sperm DNA at65° C. for 1 h in a rotating chamber. After washing in 300 mM bicine, pH8.0, 10 mM MgCl₂, 0.1% SDS with or without 10% formamide for 10 min at25° C. or for 10 min at 50° C. The array was imaged on an Olympus ProvisAX70 microscope using a 100 W mercury burner, a Texas Red filter cube,and a Princeton Instruments TEK512/CCD camera. The 16-bit greyscaleimages were captured using MetaMorph Imaging System (Universal ImagingCorporation) and rescaled to more narrowly bracket the LDR signal beforeconversion to 8-bit greyscale. The 8-bit images were inverted usingAdobe Photoshop to render the Cy3 signal black.

Example 4—p53 Chip Hybridization Showing the Presence of Mutations inDNA from Colon Tumors

A p53 chip can detect the presence of 75 different mutations in exons 5,6, 7 and 8 and uses 144 LDR oligonucleotides (see Table 5). FIG. 24 isan example of microarray-based p53 mutation detection using DNA derivedfrom colon tumors. The mutation status of each sample and the zip-codesexpected to capture signal are indicated to the right of each panel. Thefigure shows Cy3 background in the lowest panel on the right that is dueto contaminating fluorescence in the spotted zip-codes (FIG. 24H). PCRwas carried out as a single-tube, multiplex reaction in order tosimultaneously amplify p53 exons 5, 6, 7, and 8. Genomic DNA extractedfrom colon tumors was amplified in a 25 μl reaction mixture containing100 ng of DNA, 400 μM of each dNTP, 1×PCR Buffer II (10 mM Tris-HCl pH8.3 at 25° C., 50 mM KCl) supplemented with 4 mM MgCl₂, 1 U AmpliTaqGold and 2 pmol of each gene-specific primer bearing either universalprimer A or B on the 5′ ends (see Table 5). The reaction was overlaidwith mineral oil and preincubated for 10 min at 95° C. Amplification wasperformed for 15 cycles as follows: 94° C. for 15 sec, 65° C. for 1 min.A second 25 μl aliquot of the reaction mixture was added through themineral oil containing 25 pmol each of universal primers A and B.Cycling was repeated using 55° C. annealing temperature. The reactionwas next digested with a 2 μl solution of 1 mg/ml Proteinase K/50 mMEDTA at 55° C. for 10 min. Proteinase K was eliminated by a finalincubation at 90° C. for 15 min. For LDR, oligonucleotide synthesis andpurification were carried out as previously described (Khanna et al.,“Multiplex PCR/LDR for Detection of K-ras Mutations in Primary ColonTumors,” Oncogene 18:27-38 (1999), which is hereby incorporated byreference). Tth DNA ligase was overproduced and purified as describedelsewhere (Luo et al., “Identification of Essential Residues in Thermusthermophilus DNA Ligase,” Nucleic Acids Research 24:3079-3085 (1996) andBarany et al., “Cloning, Overexpression, and Nucleotide Sequence of aThermostable DNA Ligase Gene,” Gene 109:1-11(1991), which are herebyincorporated by reference). LDR was performed in a 20 μl reactioncontaining 500 fmol of each probe, 2 μl of amplified DNA and 20 mMTris-HCl, pH 7.6; 10 mM MgCl₂; 100 mM KCl; 10 mM DTT; 1 mM NAD⁺. Tworeactions were performed for each sample containing LDR probes that weredesigned to hybridize to the upper strand or lower strand of p53sequence. The reaction was heated to 94° C. for 1.5 min prior to adding25 fmol of Tth DNA ligase and then subjected to 20 cycles of 15 sec at94° C. and 4 min at 65° C. (See Table 5) LDR reactions were hybridizedin 32 μl containing 100 μg/ml sheared salmon sperm DNA 300 mM MES, pH6.0, 10 mM MgCl₂, 0.1% SDS at 65° C. for 1 h in a rotating chamber.After washing in 300 mM bicine, pH 8.0, 10 mM MgCl₂ 0.1% SDS for 10 minat 50° C. The array was imaged on an Olympus Provis AX70 microscopeusing a 100 W mercury burner, a Texas Red filter cube, and a PrincetonInstruments TEK512/CCD camera. The 16-bit greyscale images were capturedusing MetaMorph Imaging System (Universal Imaging Corporation) andrescaled to more narrowly bracket the LDR signal before conversion to8-bit greyscale. Using Adobe Photoshop, the 8-bit images were firstinverted to render the Cy3 signal black and then the images for eachsample derived from hybridization using LDR targeted to the upper strandand lower strand of the p53 sequence were overlaid and merged. Theresults of this procedure are shown in FIG. 24.

Example 5—Optimized Zipcode Sequence Construction Using Tetramers

The universal DNA array is designed on the concept of using divergentsequences to uniquely tag LDR products such that each one is captured ata unique site. The heart of the concept is the design of 36 tetramers,each of which differs from any other by at least 2 bases (See Table 6).

TABLE 6 Original New tetramer Tetramer Tetramer tetramer designationsequence complement G + C designation (See Table 1) 5′-3′ 5′-3′ bases 16 TTGA TCAA 1 2 7 TGAT ATCA 1 3 8 TTAG CTAA 1 4 26 AATC GATT 1 5 31 ATACGTAT 1 6 32 AAAG CTTT 1 7 36 TACA TGTA 1 8 1 TCTG CAGA 2 9 2 TGTC GACA 210 5 TCGT ACGA 2 11 9 CTTG CAAG 2 12 10 CGTT AACG 2 13 11 CTCA TGAG 2 1413 CTGT ACAG 2 15 15 CCAT ATGG 2 16 16 CGAA TTCG 2 17 17 GCTT AAGC 2 1818 GGTA TACC 2 19 19 GTCT AGAC 2 20 21 GAGT ACTC 2 21 23 GCAA TTGC 2 2225 AGTG CACT 2 23 27 ACCT AGGT 2 24 28 ATCG CGAT 2 25 30 AGGA TCCT 2 2633 CCTA TAGG 2 27 34 GATG CATC 2 28 3 TCCC GGGA 3 29 4 TGCG CGCA 3 30 12CACG CGTG 3 31 14 CAGC GCTG 3 32 20 GACC GGTC 3 33 22 GTGC GCAC 3 34 24GGAC GTCC 3 35 29 ACGG CCGT 3 36 35 AGCC GGCT 3By combining these 36 tetramers in sets of six, addresses that are 24bases long can be constructed.

A 1296 array can be designed based on the concept of alternating tilingof given sets of tetramers. These capture oligonucleotides differed fromtheir neighbors at three alternating positions, but were the same at theother three positions, i.e. (First=A, third=C, and fifth=E positions).Thus, each capture oligonucleotide differed from any other one by atleast 6 out of 24 positions. Moreover, these differences weredistributed across the length of the capture oligonucleotides. Whenaligning a correct capture oligonucleotide with an incorrect address,the Tm differences were predicted to be greater than 24° C.Nevertheless, one of the possibilities with this type of design is forthree contiguous tetramers in a given set of positions (i.e. ABC) tomatch another capture oligonucleotide, but at a different set ofpositions (i.e. BCD).

Since optimal surfaces are three-dimensional porous surfaces, a givenLDR product has numerous opportunity to be captured at the correctaddress. Even if an LDR product transiently dissociates from a givenoligonucleotide within the correct address, it will rapidly find andhybridize to another oligonucleotide within the same address. Inpreliminary studies, it was found that changes which would be expectedto alter Tm, (i.e. use of propynyl derivatives) did not markedly affectyield of correctly hybridized products. Thus, hybridization may bekinetically controlled. In order to minimize the possibility of even lowlevels of cross-hybridization between two closely related captureoligonucleotides, the sequences can be designed to maximize differencesamong the tetramer order with a 24 mer capture oligonucleotide.

The process for designing such sequences is outlined below:

1. Create three columns containing all 46,656 (=36×36×36) permutationsof three sets of the 36 tetramers.

2. Compute the Tm of the 46,656 12-mers using the Oligo 6.0 program fromMolecular Biology Insights, Inc. (Cascade, Colo.) and sort the listaccording to predicted Tm values.

3. Remove 12-mers that contain one GC base (Tetramers #1-7) in eachtetramer or contain three GC bases in each tetramer (Tetramers #28-36).This process removes the extremes in Tm range. Remove 12-mers with Tmvalues less than 24° C. Remove the remaining 12-mers that have threerepeated tetramers (i.e. 9-9-9)

4. Group the set of 12-mers by Tm with a new group for each 2 degreesincrease in Tm. Values were set by dividing Tm by two and truncating towhole numbers.

5. Randomize list and split into odd and even 12-mers. Invert secondlist and append to the end of first list to form 6 tetramers=12,880address candidates. Concatenate sequences and determine Tm values of24-mers.

6. Select only hexa-tetramers with Tm values between 75 and 84.

Reclaim unused trimers and make new hexa-tetramers with increased Tm andadd back to list.

7. The lists were pruned using the 13 selection conditions as describedin Table 7: A “1” indicates a match at that position, a “0” indicates nomatch. Anytime two candidate addresses matched at one of the conditions,it was removed from the candidate list and returned to the unused trimerlist.

TABLE 7 Condition Tetramer 1 Tetramer 2 Tetramer 3 Tetramer 4 Tetramer 5Tetramer 6 L Four in a row 1 1 1 1 0 0 M Four in a row 0 1 1 1 1 0 RFour in a row 0 0 1 1 1 1 L Three in a row 1 1 1 0 0 0 M Three in a row0 1 1 1 0 0 M Three in a row 0 0 1 1 1 0 R Three in a row 0 0 0 1 1 1Interrupted 4-1 1 1 0 1 1 0 Interrupted 4-2 1 1 0 0 1 1 Interrupted 4-30 1 1 0 1 1 Interrupted 4-4 1 0 1 0 1 1 Interrupted 4-5 1 1 0 1 0 1Interrupted 4-6 1 0 1 1 0 1

8. The above 13 selection conditions reduced the list to 9,650 addresscandidates.

9. The above 13 selection conditions remove matches of four in a row andthree in a row which are in the same alignment as one another; however,they do not remove sequences which are similar but shifted over by oneor two tetramer units. In order to eliminate those kinds of artifacts,the sequences were copied below the original 6 tetramers, offset by atetramer or two as in Table 8 below:

TABLE 8 Condition Position A Position B Position C Position D Position EPosition F Four in a row + 1 Position A Position B Position C Position DFour in a row + 2 Position A Position B Position C Position D Four in arow − 1 Position C Position D Position E Position F Four split − 1Position B Position C Position E Position F

10. These three selections culled the list to 8,894 candidate captureoligonucleotides, 4,798 more than the target of 4,096 for a 64×64address array. These capture oligonucleotide sequences have thefollowing properties: (1) there are no cases of 4 tetramers in a rowwhich are identical, either when capture oligonucleotide sequences arealigned with each other, or when they are offset with respect to eachother or split with respect to each other; (2) there are no cases of 3tetramers in a row which are identical, when capture oligonucleotidesequences are aligned with each other from one end; and (3) there are nocases where four out of six tetramers are in the same position.

11. For further selection, sequences of three in a row which were offsetwere eliminated as in Table 9 below.

TABLE 9 Condition Position A Position B Position C Position D Position EPosition F Three in a row + 1 Position A Position B Position C Three ina row + 2 Position A Position B Position C Three in a row + 3 Position APosition B Position C Three in a row + 1 Position B Position C PositionD Three in a row + 2 Position B Position C Position D Three in a row + 1Position C Position D Position E

12. These six selections culled the list to 3,038 candidate captureoligonucleotides, more than a more selective target of 2,500 for a 50×50address array. These capture oligonucleotide sequences have thefollowing properties: (1) there are no cases of 4 tetramers in a rowwhich are identical, either when capture oligonucleotide sequences arealigned with each other, or when they are offset with respect to eachother; (2) there are no cases of 3 tetramers in a row which areidentical, when capture oligonucleotides sequences are aligned with eachother from one end, or when they are offset with respect to each other;and (3) there are no cases where four out of six tetramers are in thesame position.

13. The order of tetramers were reversed and new Tm values werecalculated, added back in (6,076), and then pruned as described in steps7-11 above. The candidate list increased only marginally to 3,270.Therefore, an approach which enriched the unused trimers was needed.

14. A list of used trimers in all positions was used to determineavailable (unused) trimers and construct new sets of hexa-tetramers. Toincrease the percent of hexa-tetramers with Tm values in the 75-84° C.range, trimers with predicted Tm values of 34-50° C. were inverted withrespect to each other and used (i.e. trimer ABC with Tm of 34 was fusedto trimer DEF with Tm of 50, trimer ABC with Tm of 38 was fused totrimer DEF with Tm of 46, etc.).

15. Sets of hexa-tetramers were constructed and the trimers generated atthe junction (i.e. positions BCD and CDE) were retested against the usedtrimer list, and those hexa-tetramers which conflicted were recycled.Those hexa-tetramers which did not conflict were added to the 3,270candidate list and resorted and pruned as described in steps 7-11. Thecandidate list was expanded to 4,035.

16. The process was reiterated two more times to generate the final listof 4,633 capture oligonucleotides (SEQ ID NOS: 1-4633) (FIG. 25, whichrefers to the tetramers in Table 6), 537 sequences more than the targetof 4,096 for a 64×64 address array. These capture oligonucleotidesequences have the following properties: (1) there are no cases of 4tetramers in a row which are identical, either when captureoligonucleotide sequences are aligned with each other, or when they areoffset with respect to each other; (2) there are no cases of 3 tetramersin a row which are identical, when capture oligonucleotide sequences arealigned with each other from one end, or when they are offset withrespect to each other; and (3) there are no cases where four out of sixtetramers are in the same position.

17. Using the 4,633 capture oligonucleotide list, smaller lists for an8×8=64 address array, 8×12=96 address array, 16×24=384 address array,and 20×20=400 address array were created. As selection criteria, captureoligonucleotides which shared pairs of tetramers in common wereselectively removed from the list. A culling of all dimer pairs whichwere the same in given positions (i.e. AB=AB) reduced the list to 465capture oligonucleotide sequences (SEQ ID NOS: 1-465) (FIG. 26, whichrefers to the tetramers in Table 6). A second culling of dimer pairssimilar among neighboring positions (i.e. AB=BC, BC=CD, etc.) andremoval of all dimer pairs used more than twice reduced the set to 96capture oligonucleotide sequences (SEQ ID NOS: 1-96) (FIG. 27, whichrefers to the tetramers in Table 6). Finally, ensuring that no dimer wasused more than once generated a list of 65 capture oligonucleotidesequences (SEQ ID NOS: 1-65) (FIG. 28, which refers to the tetramers inTable 6).

18. The capture oligonucleotides can also be in the form of PNA (i.e.Peptide Nucleotide Analogues), as shown in FIG. 29 (which refers to thetetramers in Table 6), which contains a list of 4633 such captureoligonucleotides (SEQ ID NOS: 4634-9266). These PNA captureoligonucleotides are in the form of 20 mer units. PNA provides theadvantage of increasing the Tm of the oligonucleotide, on average 1.0°C. to 1.5° C. per base, so the Tm values of the oligomers listed in FIG.29 would be on average 20° C. (or more) higher when synthesized as thePNA form. Thus, the addresses would only need to be 20mers or less inthe PNA form. These sequences are amenable to a more rapid synthesis byconsidering two alternative approaches. In the first approach, the 36tetramers listed in Table 6 are initially synthesized, and then 5tetramers linked in the correct order to form the sequences listed inFIG. 29. Alternatively, the PNA oligomers would be synthesized using alithographic synthesis approach. A standard lithographic synthesis woulduse the 4 bases over and over again, i.e. A-C-G-T for the firstposition, A-C-G-T for the second position, etc., and would require4×20=80 masks. The current sequences listed in FIG. 29 are amenable tosynthesis in 62 masks, or less by altering the order of masks. The 62masks would allow attachment of the PNA monomers in the following order:

(SEQ ID NO: 9536) T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G

For a given sequence, the mask at the next base which allows thatsequence is opened over that address. By way of example, if thenucleotide sequence of SEQ ID NO:9536 were shortened to be the first 20nucleotides of SEQ ID NO:9536, it could be finished using just 20 masks.Different sequences will require more masks. Thus, the 20-mers arefinished with different numbers of masks. Examples are provided belowfor synthesis of 5 different addresses Zip ID#s 1, 2, 3, 4, and 26 whichrequire less than 62 masks. In these examples, use of a mask isdesignated by an underlining of that base to achieve the correctsequence.

Zip ID#1. (SEQ ID NO: 9545) AATCCAGCGCAAAATCTGCG = 45 masks(SEQ ID NO: 9536) T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G Zip ID#2. (SEQ ID NO: 9546)AAAGCCTACACGACGGCGAA = 56 masks (SEQ ID NO: 9536)T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G Zip ID#3. (SEQ ID NO: 9547)TCTGCCATACGGGCTTACGG = 50 masks (SEQ ID NO: 9536)T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G Zip ID#4. (SEQ ID NO: 9548)CTTGTCCCCAGCACGGCCAT = 49 masks  (SEQ ID NO: 9536)T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G Zip ID#26. (SEQ ID NO: 9549)TCGTCGTTTCCCCTCATGCG = 54 masks (SEQ ID NO: 9536)T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-G-C-A-T-G-C-A-G-T-C-A-T-GThis demonstrates that PNA addresses of 20 mers may be synthesized usinga lithographic approach with no more than 62 masks, far less than the 80masks required by the standard approach to synthesize a 20mer, and evenless than the 64 masks required to make a standard PNA 16 mer.

All addresses were selected to have Tm values between 75 and 84° C. Thedistribution of Tm values is more or less independent of captureoligonucleotide number. While addresses with higher G+C content ingeneral gave higher Tm values, the simple Tm=4(G+C)+2(A+T) rule was offby up to 10° C. in many cases. The values for the 96, 465, and 4633capture oligonucleotides is shown in FIGS. 30, 31, and 32, respectively.Sorted Tm values of the 4633 list of capture oligonucleotide probes areshown in FIG. 33. The gradient of Tm values was relatively even, withthe majority of capture oligonucleotides (80%) having Tm values from andincluding 75° C. to 80° C. FIG. 34 shows tetramer usage in the lists of65, 96, 465, and 4633 capture oligonucleotides produced in accordancewith the present invention. If tetramer distribution was completelyrandom, each tetramer should be represented 2.7% of the time. However,selection was biased towards higher Tm capture oligonucleotide probes.Thus, tetramers which tend to increase the Tm values, i.e. #29=TGCG areover-represented, while tetramers which tend to decrease the Tm values,i.e. #7=TACA are under-represented.

The present approach to mutation detection has three orthogonalcomponents: (i) primary PCR amplification; (ii) solution-phase LDRdetection; and (iii) solid-phase hybridization capture. Therefore,background signal from each step can be minimized, and, consequently,the overall sensitivity and accuracy of the present method issignificantly enhanced over those provided by other strategies. Forexample, “sequencing by hybridization” methods require: (i) multiplerounds of PCR or PCR/T7 transcription; (ii) processing of PCR amplifiedproducts to fragment them or render them single-stranded; and (iii)lengthy hybridization periods (10 h or more) which limit theirthroughput (Guo, et al., Nucleic Acids Res 22:5456-5465 (1994); Hacia,et. al., Nat. Genet., 14441-447 (1996); Chee, et al., Science,274:610-614 (1996); Cronin, et al., Human Mutation, 7:244-255 (1996);Wang, et al., Science, 280:1077-1082 (1998); Schena, et al., Proc. Natl.Acad. Sci. USA, 93:10614-10619 (1996); and Shalon, et al., Genome Res.,6:639-645 (1996), which are hereby incorporated by reference).Additionally, since the immobilized probes on these arrays have a widerange of T.'s, it is necessary to perform the hybridizations attemperatures from 0° C. to 44° C. The result is increased backgroundnoise and false signals due to mismatch hybridization and non-specificbinding, for example on small insertions and deletions in repeatsequences (Hacia, et. al., Nat. Genet., 14441-447 (1996); Cronin, etal., Human Mutation, 7:244-255 (1996); Wang, et al., Science,280:1077-1082 (1998); and Southern, E. M., Trends in Genet., 12:110-115(1996), which are hereby incorporated by reference). In contrast, theapproach of the present invention allows multiplexed PCR in a singlereaction (Belgrader, et al., Genome Sci. Technol., 1:77-87 (1996), whichis hereby incorporated by reference), does not require an additionalstep to convert product into single-stranded form, and can readilydistinguish all point mutations including slippage in repeat sequences(Day, et al., Genomics, 29:152-162 (1995), which is hereby incorporatedby reference). Alternative DNA arrays suffer from differentialhybridization efficiencies due to either sequence variation or to theamount of target present in the sample. By using the present approach ofdesigning divergent address sequences with similar thermodynamicproperties, hybridizations can be carried out at 65° C., resulting in amore stringent and rapid hybridization. The decoupling of thehybridization step from the mutation detection stage offers the prospectof quantification of LDR products, as has already been achieved usinggel-based LDR detection.

Arrays spotted on polymer surfaces provide substantial improvements insignal capture, as compared with arrays spotted or synthesized in situdirectly on glass surfaces (Drobyshev, et al., Gene, 188:45-52 (1997);Yershov, et al., Proc. Natl. Acad. Sci. USA, 93:4913-4918 (1996); andParinov, et al., Nucleic Acids Res., 24:2998-3004 (1996), which arehereby incorporated by reference). However, the polymers described byothers are limited to using 8- to 10-mer addresses while the polymericsurface of the present invention readily allows 24-mer captureoligonucleotides to penetrate and couple covalently. Moreover, LDRproducts of length 60 to 75 nucleotide bases are also found to penetrateand subsequently hybridize to the correct address. As additionaladvantages, the polymer gives little or no background fluorescence anddoes not exhibit non-specific binding of fluorescently-labeledoligonucleotides. Finally, capture oligonucleotides spotted and coupledcovalently at a discrete address do not “bleed over” to neighboringspots, hence obviating the need to physically segregate sites, e.g., bycutting gel pads.

The present invention relates to a strategy for high-throughput mutationdetection which differs substantially from other array-based detectionsystems presented previously in the literature. In concert with apolymerase chain reaction/ligase detection reaction (PCR/LDR) assaycarried out in solution, the array of the present invention allows foraccurate detection of single base mutations, whether inherited andpresent as 50% of the sequence for that gene, or sporadic and present at1% or less of the wild-type sequence. This sensitivity is achieved,because thermostable DNA ligase provides the specificity of mutationdiscrimination, while the divergent addressable array-specific portionsof the LDR probes guide each LDR product to a designated address on theDNA array. Since the address sequences remain constant and theircomplements can be appended to any set of LDR probes, the addressablearrays of the present invention are universal. Thus, a single arraydesign can be programmed to detect a wide range of genetic mutations.

Robust methods for the rapid detection of mutations at numerouspotential sites in multiple genes hold great promise to improve thediagnosis and treatment of cancer patients. Noninvasive tests formutational analysis of shed cells in saliva, sputum, urine, and stoolcould significantly simplify and improve the surveillance of high riskpopulations, reduce the cost and discomfort of endoscopic testing, andlead to more effective diagnosis of cancer in its early, curable stage.Although the feasibility of detecting shed mutations has beendemonstrated clearly in patients with known and geneticallycharacterized tumors (Sidransky, et al., Science, 256:102-105 (1992),Nollau, et al., Int. J. Cancer, 66:332-336 (1996); Calas, et al., CancerRes. 54:3568-73 (1994); Hasegawa, et al., Oncogene 10:1413-16 (1995);and Wu et al., Early Detection of Cancer Molecular Markers (Lippman, etal. ed.) (1994), which are hereby incorporated by reference), effectivepresymptomatic screening will require that a myriad of potential lowfrequency mutations be identified with minimal false-positive andfalse-negative signals. Furthermore, the integration of technologies fordetermining the genetic changes within a tumor with clinical informationabout the likelihood of response to therapy could radically alter howpatients with more advanced tumors are selected for treatment.Identification and validation of reliable genetic markers will requirethat many candidate genes be tested in large scale clinical trials.While costly microfabricated chips can be manufactured with over 100,000addresses, none of them have demonstrated a capability to detect lowabundance mutations (Hacia, et. al., Nat. Genet., 14441-447 (1996);Chee, et al., Science, 274:610-614 (1996); Kozal, et al., Nat. Med.,2:753-759 (1996); and Wang, et al., Science, 280:1077-1082 (1998), whichare hereby incorporated by reference), as required to accurately scoremutation profiles in such clinical trials. The universal addressablearray approach of the present invention has the potential to allow rapidand reliable identification of low abundance mutations in multiplecodons in numerous genes, as well as quantification of multiple genedeletions and amplifications associated with tumor progression. Inaddition, for mRNA expression profiling, the LDR-universal array candifferentiate highly homologous genes, such as K-, N-, and H-ras.Moreover, as new therapies targeted to specific genes or specific mutantproteins are developed, the importance of rapid and accuratehigh-throughput genetic testing will undoubtedly increase.

Example 6—Computer Software for Designing Addressable Array to AvoidBinding to Target Sequence

In designing an addressable array, it is important to insure that thetarget sequence does not hybridize to capture probes on the array. Asdescribed below, a computer program has been designed for this purpose.The program locates stretches of sequence that match any of the arraysequences at N−x of N adjacent nucleotide positions. The parameters xand N are set by the user.

The program sends output to the screen and to a file. The screen outputsummarizes the number of sequences comparisons where the longest matchwas i of M bases, where M is greater than or equal to N, and where i isgreater than or equal to M−x. The output file shows the actual match foreach sequence pair, as well as giving the summary information providedon the screen. An example of the file output is shown below.

Input file 1: kraspoly.dos Input file 2: zip64.dosMinimum number of sites that must match:  7Maximum number of mismatches allowed:  2 7 out of 8 K-rasc32Wtattcagaatc(ATTTTGtG)gacgaa (SEQ ID NO: 9537) ZIP1cgcag(ATTTTGcG)ctggatttcaa (SEQ ID NO: 9538) 7 out of 9 K-rasc32Wtattcagaatcattt(TGtGGACgA)a (SEQ ID NO: 9539) ZIP4atggccgtgc(TGgGGACaA)gtcaa (SEQ ID NO: 9540) <... deleted output... >7 out of 8 K-rasc13.4D tgtggtagt(TGgAGCTG)gtga (SEQ ID NO: 9541) ZIP61ggctcgtg(TGtAGCTG)ccgttcct (SEQ ID NO: 9542) 7 out of 8 K-rasc13.4Dtgtggtagttg(GAGcTGGT)ga (SEQ ID NO: 9543) ZIP62ggtcaagcgct(GAGgTGGT)ccatc (SEQ ID NO: 9544) SUMMARY OF ANALYSISComparisons with 1 mismatch 8 out of 9 bases matching: 107 out of 8 bases matching:  9 Comparisons with 2 mismatches9 out of 11 bases matching:  2 8 out of 10 bases matching: 277 out of 9 bases matching: 36A total of 84 out of 520 sequence comparisons met the match criteria.The area within the parentheses represents the longest identified match,with upper-case alleles representing the actual matched sites andlower-case alleles representing the allowed mismatches.

The program has been written in ANSI C for the purpose of portabilityacross platforms. The precise software used is set forth in FIG. 35. Theprogram accepts input files in straight text format. Sequences mayinclude standard ambiguity codes (e.g., the code Y corresponds to eitherC or T).

Each of F₁ sequences in Input File #1 is compared to each of F₂ sequencein File #2, for a total of F₁×F₂ comparisons. For each pair, the twosequences are compared N consecutive sites at a time in all possiblealignments. If a match of at least N−x out of N adjacent sites isdetected, the number of sites compared is incremented by one (i.e.,after i increments, the match criteria become N−x+i out of N+i sites).This process is repeated until no matches meeting the match criteria arefound. The longest match for a sequence pair is defined as the matchinvolving the longest value of N+i, as opposed to the longest value ofN−x+i. Therefore, users are explicitly should repeat all analyses withdifferent levels of stringency (i.e., x=0, x=1, x=2, . . . ). This isimportant if the user is concerned with the possibility that a perfect,or near-perfect, match might be masked by a less perfect match over alonger stretch. For example, 7 out of 7 matched sites would not bereported if (i) a pair of sequences matched at 8 out of 10 sites and(ii) if the match criterion allowed 2 mismatches.

Although the invention has been described in detail for the purpose ofillustration, it is understood that such details are solely for thatpurpose and variations can be made therein by those skilled in the artwithout departing from the spirit and scope of the invention which isdefined by the following claims.

1. (canceled)
 2. An apparatus comprising: a solid support having anarray of positions; a collection of composite or encodedoligonucleotides coupled to the solid support at the array of positions,each of said composite or encoded oligonucleotides characterized byhaving a target-specific portion and an address, wherein the addresscomprises two multimer unit sequences coupled to the solid support,wherein each multimer unit sequence (1) is comprised of threeconsecutive subunits linked together, each subunit independentlyselected from the group consisting of a trimer, tetramer, pentamer, orhexamer sequence, (2) differs from other multimer unit sequences by atleast two nucleotide bases in at least one of the subunits when aligned,and (3) has a Tm value greater than 24° C., wherein the collection ofoligonucleotides has at least 64 different types of oligonucleotides,and wherein the collection of composite or encoded oligonucleotides doesnot contain: (1) composite or encoded oligonucleotides having an addresswith a melting temperature in ° C. less than 11 times the number ofsubunits, (2) composite or encoded oligonucleotides having an addresscomprised of two identical multimer unit sequences linked together and(3) two types of composite or encoded oligonucleotides with an addresshaving the same four subunit sequences linked together in the same orderwithout interruption; and one or more detectable labels coupled to atleast one of the composite or encoded oligonucleotides, therebyfacilitating detection of the composite or encoded oligonucleotide andits address.
 3. The apparatus of claim 2 further comprising: an imagerfor detecting or quantifying at least one of the detectable labels atleast one of the array positions on the solid support.
 4. The apparatusof claim 3, wherein the composite or encoded oligonucleotides arecoupled to spheres.
 5. The apparatus of claim 3, wherein differentcomposite or encoded oligonucleotides are coupled to the solid supportat different array positions.
 6. The apparatus of claim 3, wherein thesolid support having an array of positions comprises a high-densityarray of composite or encoded oligonucleotides immobilized thereto. 7.The apparatus of claim 3, wherein the solid support is made from amaterial selected from the group consisting of plastic, ceramic, metal,gel, glass, silicon, and composites thereof.
 8. The apparatus of claim3, wherein the solid support is in a form selected from the groupconsisting of slides, discs, membranes, and films.
 9. The apparatus ofclaim 3, wherein the address of the composite or encoded oligonucleotidecomprises a nucleotide sequence that is complementary to a secondaryoligonucleotide probe, and the target specific sequence comprises anucleotide sequence that is the same as, or complementary to, a targetnucleotide sequence in a sample.
 10. The apparatus of claim 9, whereinthe target nucleotide sequence in the sample comprises an amplificationproduct, or complement thereof, of one or more target nucleic acidsequences.
 11. The apparatus of claim 3, wherein the imager is afluorescence imager and the detectable label is a fluorescent labelsuitable for detection by the fluorescence imager.
 12. The apparatus ofclaim 3, wherein the one or more detectable labels is indicative of thetarget-specific sequence included within the composite or encodedoligonucleotide to which it is coupled.
 13. The apparatus of claim 3,wherein the one or more detectable labels is indicative of a nucleicacid sequence in a sample that is the same as, or complementary to, thetarget-specific sequence included within the composite or encodedoligonucleotide to which it is coupled.
 14. The apparatus of claim 3,wherein the one or more detectable labels is coupled to the address ofthe composite or encoded oligonucleotide in a target specific manner byan enzyme.
 15. The apparatus of claim 3, wherein detection of one ormore detectable labels coupled to the address of the composite orencoded oligonucleotides correlates to the presence of one or moretarget nucleic acid sequences in the sample that is the same as, orcomplementary to the target-specific portion of the composite or encodedoligonucleotide.
 16. The apparatus of claim 3, wherein detection,identification, and quantification of the one or more detectable labelscorrelates to the presence, identity, or quantity of one or more targetnucleic acid sequences in a sample.
 17. The apparatus of claim 4,wherein the group of spheres has greater than 4,000 composite or encodedoligonucleotides.
 18. A device comprising: a solid support having anarray of positions each suitable for attachment of one or more of acollection of oligonucleotides; an array of oligonucleotides on thesolid support at the array of positions, wherein the one or more of acollection of oligonucleotides on the solid support comprises twomultimer unit sequences coupled to the solid support, wherein eachmultimer unit sequence is comprised of three consecutive subunits linkedtogether, each subunit independently selected from the group consistingof a trimer, tetramer, pentamer, or hexamer sequence, wherein eachmultimer unit sequence has a Tm value of greater than 24° C., whereineach of the two multimer unit sequences differs from all other multimerunit sequences by at least two nucleotide bases in at least one subunitwhen aligned, wherein the collection of oligonucleotides has at least 64different types of oligonucleotides, and wherein the collection ofoligonucleotides does not contain: (1) oligonucleotides having asequence with a melting temperature in ° C. less than 11 times thenumber of subunits, (2) oligonucleotides having a sequence comprised oftwo identical multimer unit sequences linked together and (3) two typesof oligonucleotides with a sequence having the same four subunitsequences linked together in the same order without interruption,wherein one or more of the oligonucleotides of the collection ishybridized to a nucleic acid molecule comprising a complementarynucleotide sequence; and wherein one or more target nucleic acidmolecules is coupled to one or more of the oligonucleotides of thecollection.
 19. A device according to claim 18, wherein identifying theoligonucleotides at the array of positions facilitates identifying theone or more target nucleic acid molecules.
 20. The device according toclaim 18 wherein the array has greater than 4,000 oligonucleotides. 21.The device according to claim 18, wherein different oligonucleotides areattached at different array positions on the solid support.
 22. Thedevice according to claim 18, wherein oligonucleotides having the samesequences are attached at different positions on the support.
 23. Thedevice according to claim 18, wherein the solid support comprisesparticles, strands, precipitates, gels, sheets, tubing, spheres,containers, capillaries, pads, slices, films, plates, slides, discs,membranes, or any combination or composite thereof.
 24. The deviceaccording to claim 18, wherein a linker couples the one or moreoligonucleotides at the array of positions to the solid support.
 25. Aninstrument comprising: a solid support comprising at least 64 types ofoligonucleotides coupled to the solid support at an array of positions,wherein the one or more oligonucleotides coupled to the solid support ata position on the array comprises an address that comprises two multimerunit sequences coupled to the solid support, wherein each multimer unitsequence (1) is comprised of three consecutive subunits linked together,each subunit independently selected from the group consisting of atrimer, tetramer, pentamer, or hexamer sequence, (2) differs from theother multimer unit sequences by at least two nucleotide bases in atleast one of the subunits when aligned, and (3) has a Tm value greaterthan 24° C., and wherein the oligonucleotides on the array do notcontain: (1) oligonucleotides having an address with a meltingtemperature in ° C. less than 11 times the number of subunits, (2)oligonucleotides having an address comprised of two identical multimerunit sequences linked together and (3) two types of oligonucleotideswith an address having the same four subunit sequences linked togetherin the same order without interruption; one or more nucleic acidmolecules hybridized to complementary portions of the one or moreoligonucleotides on said solid support; and an imager configured todetect the hybridized nucleic acid molecules.
 26. The instrument ofclaim 25, wherein the solid support comprises a high-density array ofgreater than 4,000 oligonucleotides immobilized thereto.
 27. Theinstrument of claim 25, wherein the one or more oligonucleotidesimmobilized on or coupled to the solid support at a position on thearray comprises a target-specific portion and an address.
 28. Theinstrument of claim 25, wherein the nucleic acid molecules compriseamplification products, or complements thereof, of one or more targetnucleic acid molecules.
 29. The instrument of claim 2, wherein theimager is a fluorescence imager and the nucleic acid moleculeshybridized to the one or more oligonucleotides on the solid support eachcomprise a fluorescent label suitable for detection by the fluorescenceimager.